Starting phenix.real_space_refine on Wed Jan 22 21:27:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxi_40853/01_2025/8sxi_40853_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxi_40853/01_2025/8sxi_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_40853/01_2025/8sxi_40853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxi_40853/01_2025/8sxi_40853.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxi_40853/01_2025/8sxi_40853_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxi_40853/01_2025/8sxi_40853_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.05, per 1000 atoms: 0.57 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: 4.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 3.10 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: 7.64 Time building geometry restraints manager: 5.18 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: 0.04 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: 2.210 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.510 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 19668 Z= 0.374 Angle : 1.004 14.587 26661 Z= 0.555 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.055 0.004 TRP I 35 HIS 0.011 0.002 HIS L 38 PHE 0.043 0.003 PHE I 93 TYR 0.053 0.003 TYR D 96 ARG 0.031 0.001 ARG E 501 *********************** 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 : 0.432 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: 0.1605 time to fit residues: 15.6710 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 : 0.418 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 : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 SER cc_start: 0.7043 (p) cc_final: 0.6807 (p) REVERT: B 536 THR cc_start: 0.8619 (p) cc_final: 0.8211 (p) REVERT: B 591 GLN cc_start: 0.9140 (tt0) cc_final: 0.8206 (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: 0.8403 (m) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0857 time to fit residues: 4.7937 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 : 0.104 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 : 0.106 Fit side-chains REVERT: C 36 TRP cc_start: 0.8744 (m100) cc_final: 0.8447 (m100) REVERT: C 48 MET cc_start: 0.8485 (mmm) cc_final: 0.8248 (mmm) REVERT: C 107 THR cc_start: 0.9103 (p) cc_final: 0.8751 (p) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2011 time to fit residues: 8.5689 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 : 0.119 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 : 0.102 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: 0.2364 time to fit residues: 8.9324 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 : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.4980 chunk 179 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 0.0030 chunk 112 optimal weight: 0.4980 chunk 138 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 540 GLN J 656 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.157523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133261 restraints weight = 6354.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136792 restraints weight = 4210.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139142 restraints weight = 3096.950| |-----------------------------------------------------------------------------| r_work (final): 0.3601 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123534 restraints weight = 2603.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126439 restraints weight = 1644.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128370 restraints weight = 1147.467| |-----------------------------------------------------------------------------| r_work (final): 0.3614 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141434 restraints weight = 1883.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144278 restraints weight = 1294.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146372 restraints weight = 998.758| |-----------------------------------------------------------------------------| r_work (final): 0.3571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113067 restraints weight = 2057.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116884 restraints weight = 1190.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119722 restraints weight = 818.652| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19668 Z= 0.224 Angle : 0.799 13.973 26661 Z= 0.430 Chirality : 0.051 0.410 2952 Planarity : 0.005 0.082 3408 Dihedral : 6.788 52.308 2634 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.91 % Favored : 93.46 % Rotamer: Outliers : 0.70 % Allowed : 4.63 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2385 helix: 1.05 (0.27), residues: 363 sheet: -0.63 (0.18), residues: 708 loop : -1.25 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 35 HIS 0.007 0.001 HIS I 249 PHE 0.028 0.003 PHE D 71 TYR 0.046 0.002 TYR H 96 ARG 0.004 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.398 Fit side-chains REVERT: A 96 TRP cc_start: 0.9138 (m100) cc_final: 0.8566 (m100) REVERT: A 104 MET cc_start: 0.8368 (tpt) cc_final: 0.8098 (tpp) REVERT: A 215 ILE cc_start: 0.8255 (mt) cc_final: 0.7976 (tt) REVERT: A 325 ASP cc_start: 0.7686 (t0) cc_final: 0.7308 (t70) REVERT: A 362 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7582 (tm-30) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.1480 time to fit residues: 15.4443 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 : 0.390 Evaluate side-chains 44 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.114 Fit side-chains REVERT: J 528 SER cc_start: 0.7611 (p) cc_final: 0.7226 (m) REVERT: J 591 GLN cc_start: 0.8919 (tt0) cc_final: 0.8393 (tp40) REVERT: J 607 ASN cc_start: 0.8435 (t0) cc_final: 0.7981 (t0) REVERT: J 623 TRP cc_start: 0.7823 (t-100) cc_final: 0.7563 (t-100) REVERT: J 638 TYR cc_start: 0.8357 (m-10) cc_final: 0.8002 (m-10) REVERT: J 655 LYS cc_start: 0.7573 (tppt) cc_final: 0.7304 (tppt) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.0807 time to fit residues: 3.9980 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 : 0.115 Evaluate side-chains 41 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: K 39 GLN cc_start: 0.6852 (tt0) cc_final: 0.5688 (tt0) REVERT: K 45 PHE cc_start: 0.7768 (m-80) cc_final: 0.5345 (p90) REVERT: K 48 MET cc_start: 0.8191 (mmm) cc_final: 0.7987 (mmm) REVERT: K 82 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6347 (mtt180) REVERT: K 100 ASP cc_start: 0.7694 (p0) cc_final: 0.7392 (p0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1705 time to fit residues: 7.5029 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 : 0.112 Evaluate side-chains 41 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6444 (mt) cc_final: 0.6123 (mt) REVERT: L 48 ILE cc_start: 0.8934 (mm) cc_final: 0.8598 (mm) REVERT: L 53 ASN cc_start: 0.7886 (t0) cc_final: 0.7575 (t0) REVERT: L 77 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8088 (ptt180) REVERT: L 78 VAL cc_start: 0.8065 (t) cc_final: 0.7839 (t) REVERT: L 88 CYS cc_start: 0.3621 (p) cc_final: 0.2606 (p) REVERT: L 103 LYS cc_start: 0.6769 (ttpt) cc_final: 0.6382 (mttp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1806 time to fit residues: 7.8598 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 : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 74 optimal weight: 0.0870 chunk 123 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 0.0040 chunk 57 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.0372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.161603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138609 restraints weight = 6659.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141889 restraints weight = 4471.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143964 restraints weight = 3334.763| |-----------------------------------------------------------------------------| r_work (final): 0.3562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127019 restraints weight = 2621.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129538 restraints weight = 1734.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131614 restraints weight = 1260.783| |-----------------------------------------------------------------------------| r_work (final): 0.3644 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146247 restraints weight = 1869.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149047 restraints weight = 1353.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150838 restraints weight = 1077.140| |-----------------------------------------------------------------------------| r_work (final): 0.3625 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117593 restraints weight = 2048.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121720 restraints weight = 1181.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124273 restraints weight = 798.722| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19668 Z= 0.274 Angle : 0.955 31.935 26661 Z= 0.491 Chirality : 0.057 0.494 2952 Planarity : 0.006 0.050 3408 Dihedral : 6.799 52.086 2634 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.28 % Favored : 94.34 % Rotamer: Outliers : 0.98 % Allowed : 4.35 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2385 helix: 0.49 (0.26), residues: 369 sheet: -0.83 (0.18), residues: 720 loop : -1.56 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.006 TRP I 45 HIS 0.015 0.003 HIS I 66 PHE 0.081 0.004 PHE E 93 TYR 0.029 0.003 TYR E 39 ARG 0.016 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 45 TRP cc_start: 0.7894 (OUTLIER) cc_final: 0.7411 (p-90) REVERT: E 66 HIS cc_start: 0.5888 (t-90) cc_final: 0.5621 (t-90) REVERT: E 100 MET cc_start: 0.8028 (ppp) cc_final: 0.7749 (ppp) outliers start: 5 outliers final: 0 residues processed: 81 average time/residue: 0.1359 time to fit residues: 14.1209 Evaluate side-chains 58 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.374 Evaluate side-chains 46 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 528 SER cc_start: 0.7358 (p) cc_final: 0.6786 (m) REVERT: F 591 GLN cc_start: 0.8888 (tt0) cc_final: 0.8441 (tp40) REVERT: F 607 ASN cc_start: 0.8650 (t0) cc_final: 0.8237 (t0) REVERT: F 630 GLN cc_start: 0.7902 (mp10) cc_final: 0.7649 (tt0) REVERT: F 638 TYR cc_start: 0.8315 (m-10) cc_final: 0.7935 (m-10) REVERT: F 654 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: F 655 LYS cc_start: 0.7860 (tppt) cc_final: 0.7475 (tppt) REVERT: F 656 ASN cc_start: 0.8885 (m-40) cc_final: 0.8537 (m-40) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.0887 time to fit residues: 4.4989 Evaluate side-chains 39 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.101 Evaluate side-chains 37 residues out of total 107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6250 (mtt180) REVERT: K 83 ARG cc_start: 0.7898 (ptt-90) cc_final: 0.7618 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2058 time to fit residues: 8.0846 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 : 0.099 Evaluate side-chains 39 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6766 (mt) cc_final: 0.6362 (mt) REVERT: L 77 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8229 (ptt180) REVERT: L 103 LYS cc_start: 0.6902 (ttpt) cc_final: 0.6453 (mttp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1460 time to fit residues: 6.1217 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 : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 152 optimal weight: 0.0870 chunk 25 optimal weight: 8.9990 chunk 154 optimal weight: 0.0060 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 172 optimal weight: 0.0670 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 131 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142820 restraints weight = 6974.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.146109 restraints weight = 4661.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.148541 restraints weight = 3429.103| |-----------------------------------------------------------------------------| r_work (final): 0.3544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122436 restraints weight = 2367.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124834 restraints weight = 1535.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126642 restraints weight = 1103.104| |-----------------------------------------------------------------------------| r_work (final): 0.3571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.164586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140435 restraints weight = 1768.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143043 restraints weight = 1283.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144860 restraints weight = 1034.950| |-----------------------------------------------------------------------------| r_work (final): 0.3584 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123144 restraints weight = 1840.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126888 restraints weight = 1113.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129592 restraints weight = 776.469| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.328 19668 Z= 0.470 Angle : 1.033 21.630 26661 Z= 0.548 Chirality : 0.055 0.544 2952 Planarity : 0.009 0.184 3408 Dihedral : 6.733 38.842 2634 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.92 % Favored : 92.58 % Rotamer: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2385 helix: -0.33 (0.25), residues: 363 sheet: -0.89 (0.17), residues: 744 loop : -1.79 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.009 TRP E 45 HIS 0.015 0.002 HIS I 66 PHE 0.051 0.003 PHE A 93 TYR 0.047 0.003 TYR H 96 ARG 0.005 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: I 66 HIS cc_start: 0.5756 (t-90) cc_final: 0.5479 (t-90) REVERT: I 84 MET cc_start: 0.8124 (tmm) cc_final: 0.7650 (tmm) REVERT: I 293 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8257 (tttp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1542 time to fit residues: 14.9277 Evaluate side-chains 57 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.409 Evaluate side-chains 47 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.108 Fit side-chains REVERT: B 528 SER cc_start: 0.6754 (p) cc_final: 0.6376 (m) REVERT: B 591 GLN cc_start: 0.8829 (tt0) cc_final: 0.8512 (tp40) REVERT: B 607 ASN cc_start: 0.8695 (t0) cc_final: 0.8384 (t0) REVERT: B 610 TRP cc_start: 0.5683 (m-10) cc_final: 0.3943 (p90) REVERT: B 626 MET cc_start: 0.6686 (tpt) cc_final: 0.6131 (tpt) REVERT: B 630 GLN cc_start: 0.7874 (mp10) cc_final: 0.7647 (tt0) REVERT: B 638 TYR cc_start: 0.8254 (m-10) cc_final: 0.7935 (m-10) REVERT: B 649 SER cc_start: 0.8907 (m) cc_final: 0.8623 (p) REVERT: B 656 ASN cc_start: 0.8793 (m-40) cc_final: 0.8505 (m110) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1094 time to fit residues: 5.8106 Evaluate side-chains 40 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.106 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 : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 82 ARG cc_start: 0.7025 (ttm110) cc_final: 0.6378 (mtt90) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2297 time to fit residues: 8.5691 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 : 0.102 Evaluate side-chains 29 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6880 (mt) cc_final: 0.6492 (tp) REVERT: H 77 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8186 (ptt180) REVERT: H 103 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6526 (mttt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1313 time to fit residues: 4.1711 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8918 > 50: distance: 1 - 2: 21.684 distance: 2 - 3: 34.580 distance: 2 - 5: 52.125 distance: 3 - 4: 5.430 distance: 3 - 8: 35.974 distance: 5 - 6: 12.905 distance: 5 - 7: 11.237 distance: 8 - 9: 22.829 distance: 9 - 10: 18.244 distance: 9 - 12: 16.215 distance: 10 - 11: 40.234 distance: 10 - 16: 16.630 distance: 12 - 13: 69.951 distance: 13 - 14: 39.721 distance: 13 - 15: 10.629 distance: 16 - 17: 43.104 distance: 17 - 20: 55.380 distance: 18 - 19: 69.363 distance: 18 - 24: 33.218 distance: 20 - 21: 43.510 distance: 21 - 22: 24.263 distance: 21 - 23: 58.422 distance: 24 - 25: 32.986 distance: 25 - 26: 38.112 distance: 25 - 28: 39.310 distance: 26 - 27: 56.714 distance: 26 - 30: 56.046 distance: 28 - 29: 40.135 distance: 30 - 31: 40.694 distance: 31 - 32: 56.649 distance: 31 - 34: 39.975 distance: 32 - 37: 55.759 distance: 34 - 35: 39.813 distance: 34 - 36: 57.036 distance: 37 - 38: 57.457 distance: 38 - 39: 55.927 distance: 38 - 41: 55.070 distance: 39 - 40: 57.059 distance: 39 - 45: 31.327 distance: 41 - 42: 40.130 distance: 42 - 43: 36.075 distance: 42 - 44: 40.846 distance: 45 - 46: 34.529 distance: 46 - 47: 47.411 distance: 46 - 49: 62.303 distance: 47 - 48: 49.724 distance: 50 - 51: 48.100 distance: 51 - 52: 57.704 distance: 51 - 54: 41.057 distance: 52 - 53: 69.128 distance: 54 - 55: 53.298 distance: 54 - 56: 3.553 distance: 57 - 58: 11.285 distance: 58 - 59: 27.855 distance: 58 - 61: 27.203 distance: 59 - 60: 49.688 distance: 59 - 62: 46.351 distance: 62 - 63: 22.151 distance: 63 - 64: 56.484 distance: 63 - 66: 40.549 distance: 64 - 65: 24.492 distance: 66 - 67: 55.474 distance: 68 - 69: 56.063 distance: 69 - 70: 50.221 distance: 69 - 72: 56.956 distance: 70 - 71: 58.286 distance: 70 - 76: 32.115 distance: 72 - 73: 5.325 distance: 73 - 74: 56.941 distance: 73 - 75: 40.366 distance: 76 - 77: 28.422 distance: 77 - 78: 47.966 distance: 77 - 80: 47.425 distance: 78 - 79: 17.216 distance: 78 - 82: 24.395 distance: 80 - 81: 20.661 distance: 82 - 83: 10.587 distance: 83 - 84: 41.458