Starting phenix.real_space_refine on Sat Jul 4 07:06:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxi_40853/07_2026/8sxi_40853_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12123 2.51 5 N 3372 2.21 5 O 3633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "B" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 4.13, per 1000 atoms: 0.21 Number of scatterers: 19257 At special positions: 0 Unit cell: (130.226, 137.218, 128.478, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 3633 8.00 N 3372 7.00 C 12123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS I 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 167 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 752.0 milliseconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 49 sheets defined 20.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.776A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.577A pdb=" N CYS A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.108A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.906A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.652A pdb=" N GLU A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 4.084A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.373A pdb=" N LYS A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.275A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.608A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.542A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.761A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.870A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.005A pdb=" N CYS E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.016A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.163A pdb=" N ASN E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.529A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.938A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.317A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.768A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.914A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 100E through 100I removed outlier: 3.573A pdb=" N TYR G 100H" --> pdb=" O GLN G 100E" (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR G 100I" --> pdb=" O ASP G 100F" (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100E through 100I' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.650A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.824A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP I 112 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 removed outlier: 3.988A pdb=" N CYS I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.947A pdb=" N LYS I 348 " --> pdb=" O ARG I 344 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.700A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.049A pdb=" N ASN I 392 " --> pdb=" O SER I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.700A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 479 removed outlier: 3.993A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 removed outlier: 4.356A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 596 removed outlier: 3.788A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.539A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.699A pdb=" N ALA J 662 " --> pdb=" O GLN J 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.955A pdb=" N PHE K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100E through 100H removed outlier: 3.756A pdb=" N TYR K 100H" --> pdb=" O GLN K 100E" (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 100E through 100H' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 3.853A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.548A pdb=" N LYS A 485 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.577A pdb=" N LYS A 146 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.405A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.337A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 359 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.666A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 421 removed outlier: 3.619A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 307 removed outlier: 4.007A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.714A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.865A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.645A pdb=" N VAL D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 493 through 497 removed outlier: 4.313A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.528A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.199A pdb=" N LYS E 168 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AC5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.290A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.348A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.782A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 466 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 301 through 307 removed outlier: 7.147A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.623A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.681A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.523A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.493A pdb=" N VAL H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'I' and resid 492 through 497 removed outlier: 4.236A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.584A pdb=" N LYS I 485 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=AD9, first strand: chain 'I' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 131 Processing sheet with id=AE2, first strand: chain 'I' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.428A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET I 434 " --> pdb=" O ILE I 424 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.275A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 271 through 274 removed outlier: 7.077A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN I 357 " --> pdb=" O GLU I 464 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE I 466 " --> pdb=" O ASN I 357 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 301 through 307 removed outlier: 7.005A pdb=" N ASN I 301 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.508A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.481A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.958A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.329A pdb=" N VAL L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 723 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6252 1.34 - 1.47: 4809 1.47 - 1.59: 8432 1.59 - 1.72: 1 1.72 - 1.84: 174 Bond restraints: 19668 Sorted by residual: bond pdb=" CA PRO I 437 " pdb=" C PRO I 437 " ideal model delta sigma weight residual 1.517 1.492 0.025 6.70e-03 2.23e+04 1.35e+01 bond pdb=" CB PRO I 76 " pdb=" CG PRO I 76 " ideal model delta sigma weight residual 1.492 1.636 -0.144 5.00e-02 4.00e+02 8.31e+00 bond pdb=" CG1 ILE E 420 " pdb=" CD1 ILE E 420 " ideal model delta sigma weight residual 1.513 1.401 0.112 3.90e-02 6.57e+02 8.19e+00 bond pdb=" CA THR E 372 " pdb=" C THR E 372 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.37e-02 5.33e+03 7.39e+00 bond pdb=" C ASN C 52 " pdb=" N PRO C 52A" ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 4.97e+00 ... (remaining 19663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 26104 2.92 - 5.83: 501 5.83 - 8.75: 37 8.75 - 11.67: 7 11.67 - 14.59: 12 Bond angle restraints: 26661 Sorted by residual: angle pdb=" CA PRO I 76 " pdb=" N PRO I 76 " pdb=" CD PRO I 76 " ideal model delta sigma weight residual 112.00 98.91 13.09 1.40e+00 5.10e-01 8.74e+01 angle pdb=" C GLY B 531 " pdb=" N ALA B 532 " pdb=" CA ALA B 532 " ideal model delta sigma weight residual 121.70 136.29 -14.59 1.80e+00 3.09e-01 6.57e+01 angle pdb=" C GLY J 531 " pdb=" N ALA J 532 " pdb=" CA ALA J 532 " ideal model delta sigma weight residual 121.70 136.19 -14.49 1.80e+00 3.09e-01 6.48e+01 angle pdb=" C ALA F 525 " pdb=" N ALA F 526 " pdb=" CA ALA F 526 " ideal model delta sigma weight residual 121.70 135.86 -14.16 1.80e+00 3.09e-01 6.18e+01 angle pdb=" C ALA B 525 " pdb=" N ALA B 526 " pdb=" CA ALA B 526 " ideal model delta sigma weight residual 121.70 135.82 -14.12 1.80e+00 3.09e-01 6.16e+01 ... (remaining 26656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10652 17.98 - 35.96: 969 35.96 - 53.94: 165 53.94 - 71.92: 36 71.92 - 89.90: 25 Dihedral angle restraints: 11847 sinusoidal: 4791 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.50 -77.50 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.08 -73.08 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 11844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2650 0.094 - 0.188: 290 0.188 - 0.282: 8 0.282 - 0.376: 1 0.376 - 0.470: 3 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CB ILE A 420 " pdb=" CA ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CG2 ILE A 420 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CB ILE A 142 " pdb=" CA ILE A 142 " pdb=" CG1 ILE A 142 " pdb=" CG2 ILE A 142 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE E 142 " pdb=" CA ILE E 142 " pdb=" CG1 ILE E 142 " pdb=" CG2 ILE E 142 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2949 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 91 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" CD GLU I 91 " 0.072 2.00e-02 2.50e+03 pdb=" OE1 GLU I 91 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU I 91 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 419 " 0.368 9.50e-02 1.11e+02 1.65e-01 1.71e+01 pdb=" NE ARG E 419 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 419 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 419 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 419 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.009 2.00e-02 2.50e+03 2.19e-02 1.19e+01 pdb=" CG TRP A 35 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " -0.002 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 157 2.57 - 3.15: 15832 3.15 - 3.73: 28488 3.73 - 4.32: 38321 4.32 - 4.90: 63423 Nonbonded interactions: 146221 Sorted by model distance: nonbonded pdb=" O ASN E 130 " pdb=" OG SER E 158 " model vdw 1.987 3.040 nonbonded pdb=" O ASN I 130 " pdb=" OG SER I 158 " model vdw 2.021 3.040 nonbonded pdb=" OG1 THR E 257 " pdb=" OG SER E 375 " model vdw 2.072 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OG1 THR H 69 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR A 257 " pdb=" OG SER A 375 " model vdw 2.112 3.040 ... (remaining 146216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.150 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 19710 Z= 0.247 Angle : 1.007 14.587 26745 Z= 0.556 Chirality : 0.056 0.470 2952 Planarity : 0.008 0.165 3408 Dihedral : 14.398 89.903 7173 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.38 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2385 helix: 0.74 (0.28), residues: 336 sheet: -0.79 (0.19), residues: 627 loop : -1.48 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 501 TYR 0.053 0.003 TYR D 96 PHE 0.043 0.003 PHE I 93 TRP 0.055 0.004 TRP I 35 HIS 0.011 0.002 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (19668) covalent geometry : angle 1.00427 / 0.55 (26661) SS BOND : bond 0.00410 / 0.28 ( 42) SS BOND : angle 1.66292 / 1.23 ( 84) hydrogen bonds : bond 0.26210 / 17.30 ( 668) hydrogen bonds : angle 9.05891 / 6.37 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8501 (tmm) cc_final: 0.8168 (ttm) REVERT: A 96 TRP cc_start: 0.9099 (m100) cc_final: 0.8707 (m100) REVERT: A 477 TRP cc_start: 0.8590 (m-90) cc_final: 0.8181 (m-90) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0686 time to fit residues: 6.7288 Evaluate side-chains 54 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.145 Evaluate side-chains 49 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 SER cc_start: 0.7043 (p) cc_final: 0.6808 (p) REVERT: B 536 THR cc_start: 0.8619 (p) cc_final: 0.8208 (p) REVERT: B 591 GLN cc_start: 0.9140 (tt0) cc_final: 0.8207 (tp40) REVERT: B 607 ASN cc_start: 0.8554 (t0) cc_final: 0.7980 (t0) REVERT: B 649 SER cc_start: 0.8664 (m) cc_final: 0.8402 (m) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0327 time to fit residues: 1.8560 Evaluate side-chains 38 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.039 Evaluate side-chains 41 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.040 Fit side-chains REVERT: C 36 TRP cc_start: 0.8744 (m100) cc_final: 0.8448 (m100) REVERT: C 48 MET cc_start: 0.8485 (mmm) cc_final: 0.8247 (mmm) REVERT: C 107 THR cc_start: 0.9103 (p) cc_final: 0.8747 (p) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.0849 time to fit residues: 3.6246 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.039 Evaluate side-chains 36 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.031 Fit side-chains REVERT: D 35 TRP cc_start: 0.7470 (m100) cc_final: 0.7040 (m-10) REVERT: D 54 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7765 (mtp180) REVERT: D 103 LYS cc_start: 0.6399 (ttpt) cc_final: 0.5958 (mttt) REVERT: D 104 LEU cc_start: 0.9087 (tt) cc_final: 0.8814 (tt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1084 time to fit residues: 4.0803 Evaluate side-chains 26 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN B 656 ASN D 53 ASN D 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131971 restraints weight = 6694.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135124 restraints weight = 4496.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137395 restraints weight = 3367.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138930 restraints weight = 2725.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140107 restraints weight = 2343.858| |-----------------------------------------------------------------------------| r_work (final): 0.3544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122067 restraints weight = 2796.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124660 restraints weight = 1818.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126523 restraints weight = 1298.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127826 restraints weight = 998.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128761 restraints weight = 814.844| |-----------------------------------------------------------------------------| r_work (final): 0.3606 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129897 restraints weight = 1819.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132497 restraints weight = 1261.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134821 restraints weight = 990.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.136108 restraints weight = 815.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136632 restraints weight = 716.227| |-----------------------------------------------------------------------------| r_work (final): 0.3458 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109729 restraints weight = 2065.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113429 restraints weight = 1203.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116156 restraints weight = 836.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118014 restraints weight = 637.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119180 restraints weight = 517.790| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19710 Z= 0.194 Angle : 0.812 13.490 26745 Z= 0.438 Chirality : 0.051 0.407 2952 Planarity : 0.006 0.089 3408 Dihedral : 6.832 50.379 2634 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.42 % Favored : 92.96 % Rotamer: Outliers : 0.70 % Allowed : 4.92 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2385 helix: 1.02 (0.26), residues: 363 sheet: -0.69 (0.18), residues: 723 loop : -1.32 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 298 TYR 0.044 0.002 TYR D 96 PHE 0.035 0.003 PHE L 71 TRP 0.050 0.003 TRP A 35 HIS 0.007 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (19668) covalent geometry : angle 0.80945 / 0.44 (26661) SS BOND : bond 0.00682 / 0.40 ( 42) SS BOND : angle 1.35991 / 0.91 ( 84) hydrogen bonds : bond 0.05885 / 3.85 ( 668) hydrogen bonds : angle 6.18012 / 4.32 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.133 Fit side-chains REVERT: A 104 MET cc_start: 0.8624 (tpt) cc_final: 0.8255 (tpp) outliers start: 3 outliers final: 0 residues processed: 74 average time/residue: 0.0607 time to fit residues: 5.5987 Evaluate side-chains 53 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.145 Evaluate side-chains 44 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.040 Fit side-chains REVERT: J 528 SER cc_start: 0.7872 (p) cc_final: 0.7512 (m) REVERT: J 591 GLN cc_start: 0.8934 (tt0) cc_final: 0.8408 (tp40) REVERT: J 607 ASN cc_start: 0.8530 (t0) cc_final: 0.8098 (t0) REVERT: J 623 TRP cc_start: 0.7940 (t-100) cc_final: 0.7641 (t-100) REVERT: J 638 TYR cc_start: 0.8399 (m-10) cc_final: 0.8045 (m-10) REVERT: J 655 LYS cc_start: 0.7593 (tppt) cc_final: 0.7323 (tppt) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0335 time to fit residues: 1.6692 Evaluate side-chains 36 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.039 Evaluate side-chains 33 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: C 52 ASN cc_start: 0.9343 (t0) cc_final: 0.9136 (t0) REVERT: C 103 TRP cc_start: 0.7949 (m-10) cc_final: 0.7663 (m-10) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0764 time to fit residues: 2.7195 Evaluate side-chains 25 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.038 Evaluate side-chains 39 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6397 (mt) cc_final: 0.6138 (mt) REVERT: L 48 ILE cc_start: 0.8972 (mm) cc_final: 0.8588 (mm) REVERT: L 53 ASN cc_start: 0.7992 (t0) cc_final: 0.7619 (t0) REVERT: L 78 VAL cc_start: 0.8128 (t) cc_final: 0.7923 (t) REVERT: L 88 CYS cc_start: 0.3651 (p) cc_final: 0.2575 (p) REVERT: L 96 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6956 (p90) REVERT: L 103 LYS cc_start: 0.6857 (ttpt) cc_final: 0.6464 (mttt) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0712 time to fit residues: 2.9643 Evaluate side-chains 32 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 0.0050 chunk 206 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 68 optimal weight: 0.0370 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 0.0010 chunk 99 optimal weight: 0.0770 overall best weight: 0.1036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN J 656 ASN L 53 ASN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139754 restraints weight = 6657.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142918 restraints weight = 4540.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145139 restraints weight = 3443.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146775 restraints weight = 2799.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147436 restraints weight = 2396.600| |-----------------------------------------------------------------------------| r_work (final): 0.3547 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129070 restraints weight = 2580.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131711 restraints weight = 1704.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133747 restraints weight = 1226.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135033 restraints weight = 937.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136077 restraints weight = 764.668| |-----------------------------------------------------------------------------| r_work (final): 0.3703 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137962 restraints weight = 1788.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141450 restraints weight = 1198.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143865 restraints weight = 879.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145831 restraints weight = 698.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147068 restraints weight = 576.596| |-----------------------------------------------------------------------------| r_work (final): 0.3626 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116073 restraints weight = 2090.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119831 restraints weight = 1224.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122342 restraints weight = 855.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123949 restraints weight = 666.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125312 restraints weight = 557.804| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19710 Z= 0.151 Angle : 0.734 10.658 26745 Z= 0.399 Chirality : 0.049 0.437 2952 Planarity : 0.004 0.041 3408 Dihedral : 6.156 37.031 2634 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.91 % Favored : 94.72 % Rotamer: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2385 helix: 0.90 (0.27), residues: 369 sheet: -0.61 (0.18), residues: 708 loop : -1.18 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 298 TYR 0.017 0.002 TYR A 191 PHE 0.027 0.002 PHE L 71 TRP 0.040 0.002 TRP I 35 HIS 0.006 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (19668) covalent geometry : angle 0.73174 / 0.40 (26661) SS BOND : bond 0.00571 / 0.34 ( 42) SS BOND : angle 1.23814 / 0.85 ( 84) hydrogen bonds : bond 0.05073 / 3.27 ( 668) hydrogen bonds : angle 5.65037 / 3.92 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: I 35 TRP cc_start: 0.6663 (m-10) cc_final: 0.6375 (m100) REVERT: I 84 MET cc_start: 0.8437 (tmm) cc_final: 0.8204 (tmm) REVERT: I 178 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8428 (mmtp) REVERT: I 473 MET cc_start: 0.8908 (tpp) cc_final: 0.8683 (tpp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.0551 time to fit residues: 5.5967 Evaluate side-chains 59 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.086 Evaluate side-chains 46 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.027 Fit side-chains revert: symmetry clash REVERT: F 528 SER cc_start: 0.7451 (p) cc_final: 0.6980 (m) REVERT: F 591 GLN cc_start: 0.8866 (tt0) cc_final: 0.8411 (tp40) REVERT: F 607 ASN cc_start: 0.8684 (t0) cc_final: 0.8234 (t0) REVERT: F 638 TYR cc_start: 0.8374 (m-10) cc_final: 0.8044 (m-10) REVERT: F 653 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8392 (tt0) REVERT: F 655 LYS cc_start: 0.7837 (tppt) cc_final: 0.7508 (tppt) REVERT: F 656 ASN cc_start: 0.8928 (m110) cc_final: 0.8655 (m-40) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0293 time to fit residues: 1.4960 Evaluate side-chains 39 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.036 Evaluate side-chains 34 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 ARG cc_start: 0.7841 (ptt180) cc_final: 0.7640 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0737 time to fit residues: 2.6991 Evaluate side-chains 26 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.038 Evaluate side-chains 40 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6663 (mt) cc_final: 0.6216 (mt) REVERT: L 53 ASN cc_start: 0.7912 (t0) cc_final: 0.7672 (t0) REVERT: L 96 TYR cc_start: 0.6633 (m-80) cc_final: 0.6185 (p90) REVERT: L 103 LYS cc_start: 0.6785 (ttpt) cc_final: 0.6310 (mttp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0626 time to fit residues: 2.6962 Evaluate side-chains 28 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 0.0570 chunk 116 optimal weight: 0.0470 chunk 176 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136771 restraints weight = 6879.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140042 restraints weight = 4676.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142512 restraints weight = 3536.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144191 restraints weight = 2866.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145302 restraints weight = 2457.255| |-----------------------------------------------------------------------------| r_work (final): 0.3572 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130485 restraints weight = 2735.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132998 restraints weight = 1823.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134896 restraints weight = 1338.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136149 restraints weight = 1046.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136930 restraints weight = 867.412| |-----------------------------------------------------------------------------| r_work (final): 0.3724 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140695 restraints weight = 1934.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143616 restraints weight = 1384.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145463 restraints weight = 1106.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146998 restraints weight = 951.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147771 restraints weight = 851.656| |-----------------------------------------------------------------------------| r_work (final): 0.3571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111653 restraints weight = 2142.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115334 restraints weight = 1250.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117918 restraints weight = 856.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119448 restraints weight = 658.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120884 restraints weight = 548.689| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19710 Z= 0.132 Angle : 0.707 10.942 26745 Z= 0.382 Chirality : 0.048 0.453 2952 Planarity : 0.004 0.058 3408 Dihedral : 5.732 28.292 2634 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.04 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2385 helix: 0.74 (0.27), residues: 369 sheet: -0.48 (0.19), residues: 681 loop : -1.41 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 617 TYR 0.018 0.001 TYR D 36 PHE 0.019 0.002 PHE D 71 TRP 0.032 0.002 TRP E 35 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (19668) covalent geometry : angle 0.70523 / 0.38 (26661) SS BOND : bond 0.00424 / 0.31 ( 42) SS BOND : angle 1.05095 / 0.73 ( 84) hydrogen bonds : bond 0.04596 / 2.98 ( 668) hydrogen bonds : angle 5.47711 / 3.80 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 35 TRP cc_start: 0.6459 (m-10) cc_final: 0.6239 (m100) REVERT: I 104 MET cc_start: 0.8508 (tpt) cc_final: 0.8202 (tpp) REVERT: I 171 LYS cc_start: 0.6406 (mptt) cc_final: 0.5954 (mmtt) REVERT: I 178 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8160 (mmtp) REVERT: I 203 GLN cc_start: 0.9065 (pp30) cc_final: 0.8519 (pp30) REVERT: I 377 ASN cc_start: 0.8840 (p0) cc_final: 0.8582 (p0) REVERT: I 480 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8286 (tt0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0641 time to fit residues: 6.0628 Evaluate side-chains 64 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.140 Evaluate side-chains 42 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.039 Fit side-chains REVERT: F 528 SER cc_start: 0.7159 (p) cc_final: 0.6722 (m) REVERT: F 591 GLN cc_start: 0.8815 (tt0) cc_final: 0.8505 (tp40) REVERT: F 607 ASN cc_start: 0.8766 (t0) cc_final: 0.8352 (t0) REVERT: F 614 TRP cc_start: 0.6473 (m-10) cc_final: 0.6085 (m-10) REVERT: F 623 TRP cc_start: 0.7086 (t-100) cc_final: 0.6851 (t-100) REVERT: F 630 GLN cc_start: 0.8063 (mp10) cc_final: 0.7849 (tt0) REVERT: F 638 TYR cc_start: 0.8422 (m-10) cc_final: 0.7894 (m-10) REVERT: F 651 ASN cc_start: 0.8867 (m110) cc_final: 0.7552 (m110) REVERT: F 655 LYS cc_start: 0.7793 (tppt) cc_final: 0.7475 (tppt) REVERT: F 656 ASN cc_start: 0.9036 (m-40) cc_final: 0.8836 (m-40) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0442 time to fit residues: 2.0954 Evaluate side-chains 36 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.043 Evaluate side-chains 35 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: K 12 LYS cc_start: 0.6726 (mmmm) cc_final: 0.6523 (mmmm) REVERT: K 63 PHE cc_start: 0.8572 (m-80) cc_final: 0.8230 (m-10) REVERT: K 82 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6492 (mtt90) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0819 time to fit residues: 3.0693 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.037 Evaluate side-chains 35 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.021 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6616 (mt) cc_final: 0.6202 (mt) REVERT: L 53 ASN cc_start: 0.8129 (t0) cc_final: 0.7790 (t0) REVERT: L 96 TYR cc_start: 0.7046 (m-80) cc_final: 0.6112 (p90) REVERT: L 103 LYS cc_start: 0.6836 (ttpt) cc_final: 0.6380 (mttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0553 time to fit residues: 2.0669 Evaluate side-chains 27 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 20 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 117 optimal weight: 0.0010 chunk 121 optimal weight: 0.0570 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.7108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 195 ASN I 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133270 restraints weight = 6998.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136726 restraints weight = 4706.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138941 restraints weight = 3527.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140725 restraints weight = 2882.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142092 restraints weight = 2495.544| |-----------------------------------------------------------------------------| r_work (final): 0.3544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126972 restraints weight = 2742.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129534 restraints weight = 1836.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131344 restraints weight = 1329.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132523 restraints weight = 1035.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133553 restraints weight = 865.238| |-----------------------------------------------------------------------------| r_work (final): 0.3703 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.166337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142125 restraints weight = 1950.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145563 restraints weight = 1281.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147698 restraints weight = 962.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149389 restraints weight = 797.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149392 restraints weight = 690.350| |-----------------------------------------------------------------------------| r_work (final): 0.3633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114043 restraints weight = 2015.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117736 restraints weight = 1194.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120244 restraints weight = 825.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121721 restraints weight = 635.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123109 restraints weight = 531.392| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19710 Z= 0.127 Angle : 0.680 10.551 26745 Z= 0.369 Chirality : 0.047 0.360 2952 Planarity : 0.004 0.045 3408 Dihedral : 5.432 23.962 2634 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2385 helix: 0.87 (0.27), residues: 363 sheet: -0.49 (0.18), residues: 690 loop : -1.32 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 419 TYR 0.024 0.001 TYR D 36 PHE 0.014 0.002 PHE L 71 TRP 0.026 0.002 TRP I 35 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (19668) covalent geometry : angle 0.67811 / 0.37 (26661) SS BOND : bond 0.00500 / 0.37 ( 42) SS BOND : angle 1.13592 / 0.81 ( 84) hydrogen bonds : bond 0.04585 / 2.99 ( 668) hydrogen bonds : angle 5.41542 / 3.75 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 171 LYS cc_start: 0.6477 (mptt) cc_final: 0.5404 (mmtt) REVERT: I 178 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8256 (mmtp) REVERT: I 203 GLN cc_start: 0.9111 (pp30) cc_final: 0.8732 (pp30) REVERT: I 480 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8069 (tt0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0703 time to fit residues: 6.1735 Evaluate side-chains 54 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.139 Evaluate side-chains 42 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: J 607 ASN cc_start: 0.8767 (t0) cc_final: 0.8422 (t0) REVERT: J 614 TRP cc_start: 0.6535 (m-10) cc_final: 0.5868 (m-10) REVERT: J 630 GLN cc_start: 0.7953 (mp10) cc_final: 0.7612 (tt0) REVERT: J 638 TYR cc_start: 0.8304 (m-10) cc_final: 0.7746 (m-10) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0410 time to fit residues: 1.9504 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.040 Evaluate side-chains 36 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 12 LYS cc_start: 0.6798 (mmmm) cc_final: 0.6503 (mmmm) REVERT: K 82 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6487 (mtt90) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1040 time to fit residues: 3.9627 Evaluate side-chains 30 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.039 Evaluate side-chains 37 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.032 Fit side-chains REVERT: L 4 LEU cc_start: 0.6593 (mt) cc_final: 0.6114 (mt) REVERT: L 53 ASN cc_start: 0.8054 (t0) cc_final: 0.7761 (t0) REVERT: L 96 TYR cc_start: 0.7439 (m-80) cc_final: 0.5928 (p90) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0607 time to fit residues: 2.4165 Evaluate side-chains 27 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 140 optimal weight: 0.0040 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 chunk 177 optimal weight: 0.0470 chunk 207 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 425 ASN ** I 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN J 653 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131037 restraints weight = 6737.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134620 restraints weight = 4391.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137158 restraints weight = 3214.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139063 restraints weight = 2566.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140096 restraints weight = 2171.541| |-----------------------------------------------------------------------------| r_work (final): 0.3519 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125510 restraints weight = 2704.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127771 restraints weight = 1829.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129340 restraints weight = 1347.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130181 restraints weight = 1068.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130979 restraints weight = 920.393| |-----------------------------------------------------------------------------| r_work (final): 0.3641 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137594 restraints weight = 1832.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140799 restraints weight = 1255.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143150 restraints weight = 972.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144129 restraints weight = 810.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145591 restraints weight = 734.748| |-----------------------------------------------------------------------------| r_work (final): 0.3633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113396 restraints weight = 2172.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116862 restraints weight = 1227.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119175 restraints weight = 808.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120710 restraints weight = 599.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121948 restraints weight = 491.680| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19710 Z= 0.145 Angle : 0.717 10.285 26745 Z= 0.386 Chirality : 0.047 0.326 2952 Planarity : 0.005 0.058 3408 Dihedral : 5.516 38.546 2634 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 0.14 % Allowed : 1.97 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2385 helix: 0.87 (0.27), residues: 360 sheet: -0.41 (0.18), residues: 705 loop : -1.37 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 419 TYR 0.031 0.002 TYR H 36 PHE 0.011 0.002 PHE L 71 TRP 0.033 0.003 TRP J 623 HIS 0.003 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (19668) covalent geometry : angle 0.71502 / 0.38 (26661) SS BOND : bond 0.00482 / 0.35 ( 42) SS BOND : angle 1.19372 / 0.83 ( 84) hydrogen bonds : bond 0.04561 / 2.99 ( 668) hydrogen bonds : angle 5.55401 / 3.83 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: I 104 MET cc_start: 0.8533 (tpt) cc_final: 0.8064 (tpp) REVERT: I 143 GLU cc_start: 0.5975 (mm-30) cc_final: 0.5604 (tp30) REVERT: I 171 LYS cc_start: 0.6584 (mptt) cc_final: 0.5395 (mmtt) REVERT: I 180 ASP cc_start: 0.7771 (m-30) cc_final: 0.7540 (m-30) REVERT: I 203 GLN cc_start: 0.9158 (pp30) cc_final: 0.8576 (pp30) REVERT: I 325 ASP cc_start: 0.7768 (t0) cc_final: 0.7260 (t0) REVERT: I 477 TRP cc_start: 0.8303 (m-90) cc_final: 0.6765 (m100) REVERT: I 480 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8106 (tt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0551 time to fit residues: 4.5734 Evaluate side-chains 53 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.138 Evaluate side-chains 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: J 607 ASN cc_start: 0.8463 (t0) cc_final: 0.8017 (t0) REVERT: J 630 GLN cc_start: 0.8016 (mp10) cc_final: 0.7789 (tt0) REVERT: J 638 TYR cc_start: 0.8263 (m-10) cc_final: 0.7829 (m-10) REVERT: J 655 LYS cc_start: 0.7590 (tppt) cc_final: 0.7266 (tppt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0396 time to fit residues: 1.6672 Evaluate side-chains 34 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.038 Evaluate side-chains 34 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.037 Fit side-chains REVERT: K 19 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7827 (tmtt) REVERT: K 82 ARG cc_start: 0.7343 (ttm110) cc_final: 0.6634 (mtt90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0929 time to fit residues: 3.3594 Evaluate side-chains 31 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.036 Evaluate side-chains 33 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.032 Fit side-chains REVERT: L 96 TYR cc_start: 0.7192 (m-80) cc_final: 0.5973 (p90) REVERT: L 105 GLU cc_start: 0.8439 (mp0) cc_final: 0.7650 (tt0) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0679 time to fit residues: 2.4077 Evaluate side-chains 26 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 211 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 173 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 overall best weight: 2.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 425 ASN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123621 restraints weight = 6798.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126893 restraints weight = 4531.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129133 restraints weight = 3384.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130869 restraints weight = 2760.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131996 restraints weight = 2362.016| |-----------------------------------------------------------------------------| r_work (final): 0.3431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125592 restraints weight = 2828.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127791 restraints weight = 1942.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129455 restraints weight = 1474.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130391 restraints weight = 1197.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130779 restraints weight = 1034.933| |-----------------------------------------------------------------------------| r_work (final): 0.3642 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132335 restraints weight = 1925.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135697 restraints weight = 1242.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138012 restraints weight = 939.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139068 restraints weight = 778.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139076 restraints weight = 696.411| |-----------------------------------------------------------------------------| r_work (final): 0.3496 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108253 restraints weight = 2145.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111529 restraints weight = 1283.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113869 restraints weight = 900.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115382 restraints weight = 692.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115867 restraints weight = 576.688| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19710 Z= 0.175 Angle : 0.708 10.287 26745 Z= 0.387 Chirality : 0.047 0.310 2952 Planarity : 0.005 0.058 3408 Dihedral : 5.539 27.823 2634 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.66 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2385 helix: 0.57 (0.26), residues: 363 sheet: -0.46 (0.19), residues: 702 loop : -1.36 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 94 TYR 0.023 0.002 TYR H 36 PHE 0.015 0.002 PHE C 45 TRP 0.038 0.004 TRP J 623 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (19668) covalent geometry : angle 0.70541 / 0.39 (26661) SS BOND : bond 0.00531 / 0.37 ( 42) SS BOND : angle 1.32212 / 0.92 ( 84) hydrogen bonds : bond 0.04662 / 3.05 ( 668) hydrogen bonds : angle 5.61198 / 3.85 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.143 Fit side-chains REVERT: I 95 MET cc_start: 0.8265 (ppp) cc_final: 0.7982 (ppp) REVERT: I 171 LYS cc_start: 0.6592 (mptt) cc_final: 0.5432 (mmtt) REVERT: I 180 ASP cc_start: 0.7817 (m-30) cc_final: 0.7433 (m-30) REVERT: I 184 LEU cc_start: 0.7921 (pt) cc_final: 0.7561 (tt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0577 time to fit residues: 4.2099 Evaluate side-chains 46 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.157 Evaluate side-chains 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: F 607 ASN cc_start: 0.8593 (t0) cc_final: 0.8129 (t0) REVERT: F 610 TRP cc_start: 0.5452 (t60) cc_final: 0.3276 (p90) REVERT: F 626 MET cc_start: 0.6010 (tpt) cc_final: 0.5771 (tpt) REVERT: F 638 TYR cc_start: 0.8424 (m-10) cc_final: 0.7922 (m-10) REVERT: F 655 LYS cc_start: 0.7980 (tppt) cc_final: 0.7609 (tppt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0336 time to fit residues: 1.4545 Evaluate side-chains 32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.040 Evaluate side-chains 36 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.038 Fit side-chains REVERT: K 19 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7907 (tmtt) REVERT: K 28 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8411 (mtp85) REVERT: K 52 ASN cc_start: 0.9287 (t0) cc_final: 0.9043 (t0) REVERT: K 82 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6707 (mtt90) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0859 time to fit residues: 3.3029 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.043 Evaluate side-chains 30 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.038 Fit side-chains REVERT: L 4 LEU cc_start: 0.6956 (mm) cc_final: 0.6165 (mt) REVERT: L 88 CYS cc_start: 0.3559 (p) cc_final: 0.3204 (p) REVERT: L 96 TYR cc_start: 0.7693 (m-80) cc_final: 0.5878 (p90) REVERT: L 103 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7489 (mmtp) REVERT: L 105 GLU cc_start: 0.8500 (mp0) cc_final: 0.7557 (tt0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0757 time to fit residues: 2.4315 Evaluate side-chains 24 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 230 optimal weight: 0.0770 chunk 211 optimal weight: 6.9990 chunk 170 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 139 optimal weight: 0.0070 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 0.0020 chunk 196 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 overall best weight: 0.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 425 ASN ** I 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132268 restraints weight = 6619.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135804 restraints weight = 4328.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138276 restraints weight = 3170.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139894 restraints weight = 2512.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141384 restraints weight = 2138.436| |-----------------------------------------------------------------------------| r_work (final): 0.3620 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131475 restraints weight = 3025.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133854 restraints weight = 2048.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135821 restraints weight = 1530.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137109 restraints weight = 1214.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137769 restraints weight = 1024.025| |-----------------------------------------------------------------------------| r_work (final): 0.3737 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137572 restraints weight = 1901.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140729 restraints weight = 1260.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142904 restraints weight = 975.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144093 restraints weight = 814.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144093 restraints weight = 727.553| |-----------------------------------------------------------------------------| r_work (final): 0.3563 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113131 restraints weight = 1983.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116464 restraints weight = 1257.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118639 restraints weight = 904.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120390 restraints weight = 715.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121793 restraints weight = 598.744| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19710 Z= 0.131 Angle : 0.693 10.323 26745 Z= 0.376 Chirality : 0.047 0.269 2952 Planarity : 0.004 0.055 3408 Dihedral : 5.336 28.250 2634 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2385 helix: 0.92 (0.28), residues: 339 sheet: -0.31 (0.19), residues: 720 loop : -1.33 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.025 0.002 TYR D 36 PHE 0.017 0.002 PHE G 32 TRP 0.048 0.003 TRP C 36 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (19668) covalent geometry : angle 0.69132 / 0.38 (26661) SS BOND : bond 0.00459 / 0.32 ( 42) SS BOND : angle 1.06381 / 0.72 ( 84) hydrogen bonds : bond 0.04433 / 2.86 ( 668) hydrogen bonds : angle 5.59378 / 3.85 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.128 Fit side-chains REVERT: A 84 MET cc_start: 0.7736 (tmm) cc_final: 0.7289 (tmm) REVERT: A 104 MET cc_start: 0.8423 (tpt) cc_final: 0.7468 (tpp) REVERT: A 171 LYS cc_start: 0.6743 (mptt) cc_final: 0.6125 (mmtt) REVERT: A 180 ASP cc_start: 0.7795 (m-30) cc_final: 0.7522 (m-30) REVERT: A 184 LEU cc_start: 0.7890 (pt) cc_final: 0.7547 (tt) REVERT: A 203 GLN cc_start: 0.9208 (pp30) cc_final: 0.8546 (pp30) REVERT: A 209 SER cc_start: 0.8558 (t) cc_final: 0.7932 (m) REVERT: A 217 TYR cc_start: 0.8249 (m-80) cc_final: 0.8001 (m-80) REVERT: A 302 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7639 (mtpp) REVERT: A 477 TRP cc_start: 0.8351 (m-90) cc_final: 0.6642 (m100) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0710 time to fit residues: 6.1260 Evaluate side-chains 51 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.148 Evaluate side-chains 41 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.037 Fit side-chains REVERT: F 522 PHE cc_start: 0.7524 (m-80) cc_final: 0.6833 (m-10) REVERT: F 607 ASN cc_start: 0.8573 (t0) cc_final: 0.8176 (t0) REVERT: F 610 TRP cc_start: 0.4946 (t60) cc_final: 0.2968 (p90) REVERT: F 638 TYR cc_start: 0.8378 (m-10) cc_final: 0.7971 (m-10) REVERT: F 646 LEU cc_start: 0.8536 (mt) cc_final: 0.8263 (mt) REVERT: F 649 SER cc_start: 0.8945 (m) cc_final: 0.8658 (p) REVERT: F 655 LYS cc_start: 0.8047 (tppt) cc_final: 0.7692 (tppt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0334 time to fit residues: 1.5962 Evaluate side-chains 34 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.038 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.038 Fit side-chains REVERT: K 28 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8348 (mtp85) REVERT: K 82 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6752 (mtt90) REVERT: K 100 ASP cc_start: 0.6958 (p0) cc_final: 0.6675 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0822 time to fit residues: 2.8284 Evaluate side-chains 31 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.043 Evaluate side-chains 37 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6778 (mm) cc_final: 0.6090 (mt) REVERT: L 61 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7763 (ptp90) REVERT: L 96 TYR cc_start: 0.7201 (m-80) cc_final: 0.5845 (p90) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0859 time to fit residues: 3.3439 Evaluate side-chains 25 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 130 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 14 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 96 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 91 optimal weight: 0.0010 overall best weight: 0.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN F 543 ASN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.165059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141342 restraints weight = 6968.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144549 restraints weight = 4716.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146868 restraints weight = 3523.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148496 restraints weight = 2844.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149166 restraints weight = 2428.113| |-----------------------------------------------------------------------------| r_work (final): 0.3644 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130527 restraints weight = 2934.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133103 restraints weight = 2029.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134892 restraints weight = 1523.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136021 restraints weight = 1233.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136919 restraints weight = 1068.930| |-----------------------------------------------------------------------------| r_work (final): 0.3719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140449 restraints weight = 1923.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143251 restraints weight = 1286.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145803 restraints weight = 1015.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146993 restraints weight = 853.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148308 restraints weight = 768.254| |-----------------------------------------------------------------------------| r_work (final): 0.3665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115643 restraints weight = 1852.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119027 restraints weight = 1229.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121662 restraints weight = 906.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123677 restraints weight = 707.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125267 restraints weight = 581.978| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19710 Z= 0.135 Angle : 0.718 10.918 26745 Z= 0.388 Chirality : 0.048 0.296 2952 Planarity : 0.004 0.051 3408 Dihedral : 5.233 26.635 2634 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.41 % Favored : 94.34 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2385 helix: 0.79 (0.28), residues: 339 sheet: -0.03 (0.19), residues: 705 loop : -1.45 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 29 TYR 0.020 0.001 TYR D 36 PHE 0.019 0.002 PHE L 71 TRP 0.063 0.003 TRP C 36 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (19668) covalent geometry : angle 0.71656 / 0.39 (26661) SS BOND : bond 0.00508 / 0.36 ( 42) SS BOND : angle 1.17654 / 0.82 ( 84) hydrogen bonds : bond 0.04534 / 2.86 ( 668) hydrogen bonds : angle 5.80601 / 4.01 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.142 Fit side-chains REVERT: I 84 MET cc_start: 0.8009 (tmm) cc_final: 0.7491 (tmm) REVERT: I 93 PHE cc_start: 0.8089 (m-80) cc_final: 0.7567 (m-10) REVERT: I 96 TRP cc_start: 0.9099 (m100) cc_final: 0.8635 (m100) REVERT: I 171 LYS cc_start: 0.6506 (mptt) cc_final: 0.5451 (mmtt) REVERT: I 180 ASP cc_start: 0.7681 (m-30) cc_final: 0.7375 (m-30) REVERT: I 184 LEU cc_start: 0.7742 (pt) cc_final: 0.7461 (tt) REVERT: I 203 GLN cc_start: 0.9157 (pp30) cc_final: 0.8543 (pp30) REVERT: I 246 GLN cc_start: 0.8973 (mt0) cc_final: 0.8573 (mm-40) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0716 time to fit residues: 6.2105 Evaluate side-chains 53 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.173 Evaluate side-chains 40 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.047 Fit side-chains REVERT: F 522 PHE cc_start: 0.7554 (m-80) cc_final: 0.6859 (m-10) REVERT: F 607 ASN cc_start: 0.8622 (t0) cc_final: 0.8163 (t0) REVERT: F 610 TRP cc_start: 0.5556 (t60) cc_final: 0.3592 (p90) REVERT: F 614 TRP cc_start: 0.6777 (m-10) cc_final: 0.5268 (m-10) REVERT: F 638 TYR cc_start: 0.8420 (m-10) cc_final: 0.7867 (m-10) REVERT: F 655 LYS cc_start: 0.8014 (tppt) cc_final: 0.7741 (tppt) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0361 time to fit residues: 1.6418 Evaluate side-chains 36 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.045 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: K 28 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8297 (mtp85) REVERT: K 82 ARG cc_start: 0.7233 (ttm110) cc_final: 0.6770 (mtt90) REVERT: K 100 ASP cc_start: 0.6766 (p0) cc_final: 0.6472 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0749 time to fit residues: 2.5837 Evaluate side-chains 30 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.036 Evaluate side-chains 34 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6594 (mm) cc_final: 0.5920 (mt) REVERT: H 48 ILE cc_start: 0.8542 (tp) cc_final: 0.8274 (tp) REVERT: H 77 ARG cc_start: 0.8347 (mmm160) cc_final: 0.8072 (mmm160) REVERT: H 96 TYR cc_start: 0.7166 (m-80) cc_final: 0.5869 (p90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0758 time to fit residues: 2.7429 Evaluate side-chains 26 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 0 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 172 optimal weight: 0.0470 chunk 224 optimal weight: 0.0670 chunk 65 optimal weight: 0.0070 chunk 161 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 543 ASN F 625 ASN I 425 ASN ** I 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137757 restraints weight = 6561.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141397 restraints weight = 4246.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143955 restraints weight = 3079.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145635 restraints weight = 2428.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147082 restraints weight = 2048.601| |-----------------------------------------------------------------------------| r_work (final): 0.3651 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129486 restraints weight = 2903.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132294 restraints weight = 1937.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133987 restraints weight = 1434.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135698 restraints weight = 1160.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136809 restraints weight = 976.573| |-----------------------------------------------------------------------------| r_work (final): 0.3723 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141324 restraints weight = 1805.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144168 restraints weight = 1254.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146321 restraints weight = 994.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147155 restraints weight = 847.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148119 restraints weight = 782.850| |-----------------------------------------------------------------------------| r_work (final): 0.3659 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116845 restraints weight = 2064.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119792 restraints weight = 1394.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122172 restraints weight = 1033.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123722 restraints weight = 813.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125058 restraints weight = 682.502| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19710 Z= 0.136 Angle : 0.719 11.811 26745 Z= 0.391 Chirality : 0.047 0.273 2952 Planarity : 0.004 0.044 3408 Dihedral : 5.187 23.624 2634 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2385 helix: 0.74 (0.28), residues: 339 sheet: -0.25 (0.19), residues: 717 loop : -1.56 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 61 TYR 0.037 0.002 TYR L 36 PHE 0.025 0.002 PHE C 45 TRP 0.063 0.002 TRP G 36 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19668) covalent geometry : angle 0.71516 / 0.39 (26661) SS BOND : bond 0.00645 / 0.42 ( 42) SS BOND : angle 1.52148 / 1.03 ( 84) hydrogen bonds : bond 0.04452 / 2.85 ( 668) hydrogen bonds : angle 5.72203 / 3.95 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.090 Fit side-chains REVERT: A 95 MET cc_start: 0.8129 (ppp) cc_final: 0.7870 (ppp) REVERT: A 96 TRP cc_start: 0.9068 (m100) cc_final: 0.8300 (m100) REVERT: A 171 LYS cc_start: 0.6646 (mptt) cc_final: 0.6066 (mmtt) REVERT: A 180 ASP cc_start: 0.7809 (m-30) cc_final: 0.7435 (m-30) REVERT: A 184 LEU cc_start: 0.7938 (pt) cc_final: 0.7577 (tt) REVERT: A 203 GLN cc_start: 0.9226 (pp30) cc_final: 0.8554 (pp30) REVERT: A 209 SER cc_start: 0.8374 (t) cc_final: 0.7704 (m) REVERT: A 362 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0530 time to fit residues: 4.2754 Evaluate side-chains 47 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.143 Evaluate side-chains 38 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.042 Fit side-chains REVERT: F 522 PHE cc_start: 0.7479 (m-80) cc_final: 0.6792 (m-10) REVERT: F 607 ASN cc_start: 0.8633 (t0) cc_final: 0.8180 (t0) REVERT: F 638 TYR cc_start: 0.8350 (m-10) cc_final: 0.7925 (m-10) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0300 time to fit residues: 1.3116 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.025 Evaluate side-chains 32 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: K 28 ARG cc_start: 0.8806 (mtp85) cc_final: 0.8313 (mtp85) REVERT: K 82 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6753 (mtt90) REVERT: K 100 ASP cc_start: 0.6700 (p0) cc_final: 0.6439 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0726 time to fit residues: 2.5146 Evaluate side-chains 31 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.038 Evaluate side-chains 33 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.035 Fit side-chains REVERT: L 48 ILE cc_start: 0.8334 (tp) cc_final: 0.8119 (tp) REVERT: L 96 TYR cc_start: 0.7442 (m-80) cc_final: 0.5787 (p90) REVERT: L 105 GLU cc_start: 0.7929 (pm20) cc_final: 0.7514 (tt0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0758 time to fit residues: 2.6759 Evaluate side-chains 25 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 220 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 219 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN F 543 ASN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.162322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138078 restraints weight = 6735.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141609 restraints weight = 4368.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143968 restraints weight = 3198.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145882 restraints weight = 2556.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147217 restraints weight = 2139.629| |-----------------------------------------------------------------------------| r_work (final): 0.3627 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129279 restraints weight = 2934.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131843 restraints weight = 2022.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133549 restraints weight = 1528.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134199 restraints weight = 1246.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135392 restraints weight = 1116.763| |-----------------------------------------------------------------------------| r_work (final): 0.3696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143209 restraints weight = 1889.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146248 restraints weight = 1281.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147837 restraints weight = 1006.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149583 restraints weight = 873.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150335 restraints weight = 774.188| |-----------------------------------------------------------------------------| r_work (final): 0.3672 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113921 restraints weight = 2056.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116770 restraints weight = 1431.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119011 restraints weight = 1086.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120623 restraints weight = 876.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121823 restraints weight = 744.976| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19710 Z= 0.143 Angle : 0.738 12.993 26745 Z= 0.396 Chirality : 0.047 0.247 2952 Planarity : 0.004 0.056 3408 Dihedral : 5.294 25.381 2634 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.16 % Favored : 94.47 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2385 helix: 0.54 (0.27), residues: 336 sheet: -0.32 (0.19), residues: 678 loop : -1.34 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 94 TYR 0.033 0.002 TYR H 36 PHE 0.021 0.002 PHE C 45 TRP 0.064 0.003 TRP K 36 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (19668) covalent geometry : angle 0.72914 / 0.39 (26661) SS BOND : bond 0.00670 / 0.44 ( 42) SS BOND : angle 2.15434 / 1.62 ( 84) hydrogen bonds : bond 0.04413 / 2.83 ( 668) hydrogen bonds : angle 5.85328 / 4.04 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2045.99 seconds wall clock time: 36 minutes 41.13 seconds (2201.13 seconds total)