Starting phenix.real_space_refine on Sun Aug 24 09:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxj_40854/08_2025/8sxj_40854.map" } resolution = 4.0 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= 0.044 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 132 5.16 5 C 12003 2.51 5 N 3327 2.21 5 O 3588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19050 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: 1 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: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} 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: 1 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: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} 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: 1 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: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Time building chain proxies: 5.52, per 1000 atoms: 0.29 Number of scatterers: 19050 At special positions: 0 Unit cell: (145.084, 134.596, 117.99, 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 132 16.00 O 3588 8.00 N 3327 7.00 C 12003 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS I 167 " distance=2.02 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 167 " - pdb=" SG CYS I 127 " distance=2.04 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=2.03 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=2.03 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 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=2.05 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: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 37 sheets defined 19.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.600A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.614A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.668A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.536A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.682A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.543A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.525A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.503A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 482 removed outlier: 3.674A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.532A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 334 through 353 removed outlier: 4.537A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.508A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 482 removed outlier: 3.666A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.527A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 546 No H-bonds generated for 'chain 'J' and resid 544 through 546' Processing helix chain 'J' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 664 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 5.220A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.637A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (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 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.434A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 304 removed outlier: 4.275A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 320 through 323 current: chain 'A' and resid 382 through 385 removed outlier: 3.967A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 421 current: chain 'A' and resid 466 through 468 Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 removed outlier: 3.898A pdb=" N ARG A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 4.170A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100B through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'E' and resid 493 through 497 removed outlier: 5.217A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.639A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.372A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.761A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 382 through 385 removed outlier: 3.901A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 414 through 421 current: chain 'E' and resid 466 through 468 Processing sheet with id=AC3, first strand: chain 'E' and resid 358 through 361 removed outlier: 3.887A pdb=" N ARG E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.171A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100B through 103 Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AC8, first strand: chain 'I' and resid 493 through 497 removed outlier: 5.223A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.640A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'I' and resid 170 through 177 Processing sheet with id=AD4, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.045A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR I 435 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 308 removed outlier: 4.034A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 316 through 323 current: chain 'I' and resid 382 through 385 removed outlier: 3.900A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 414 through 421 current: chain 'I' and resid 466 through 468 Processing sheet with id=AD6, first strand: chain 'I' and resid 358 through 361 removed outlier: 3.893A pdb=" N ARG I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.146A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100B through 103 Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 553 hydrogen bonds defined for protein. 1476 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: 3.64 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.52: 12474 1.52 - 1.83: 6982 1.83 - 2.14: 0 2.14 - 2.45: 0 2.45 - 2.76: 2 Bond restraints: 19458 Sorted by residual: bond pdb=" C TRP H 94 " pdb=" N TRP H 96 " ideal model delta sigma weight residual 1.331 2.765 -1.434 1.51e-02 4.39e+03 9.02e+03 bond pdb=" C TRP L 94 " pdb=" N TRP L 96 " ideal model delta sigma weight residual 1.331 2.763 -1.432 1.51e-02 4.39e+03 8.99e+03 bond pdb=" CZ ARG K 66 " pdb=" NH2 ARG K 66 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG G 66 " pdb=" NH2 ARG G 66 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG C 66 " pdb=" NH2 ARG C 66 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 19453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 26228 5.04 - 10.09: 171 10.09 - 15.13: 5 15.13 - 20.18: 0 20.18 - 25.22: 2 Bond angle restraints: 26406 Sorted by residual: angle pdb=" O TRP H 94 " pdb=" C TRP H 94 " pdb=" N TRP H 96 " ideal model delta sigma weight residual 121.20 95.98 25.22 1.61e+00 3.86e-01 2.45e+02 angle pdb=" O TRP L 94 " pdb=" C TRP L 94 " pdb=" N TRP L 96 " ideal model delta sigma weight residual 121.20 96.28 24.92 1.61e+00 3.86e-01 2.40e+02 angle pdb=" C TRP L 94 " pdb=" N TRP L 96 " pdb=" CA TRP L 96 " ideal model delta sigma weight residual 122.62 109.69 12.93 1.56e+00 4.11e-01 6.87e+01 angle pdb=" C TRP H 94 " pdb=" N TRP H 96 " pdb=" CA TRP H 96 " ideal model delta sigma weight residual 122.62 109.91 12.71 1.56e+00 4.11e-01 6.64e+01 angle pdb=" N LYS A 356 " pdb=" CA LYS A 356 " pdb=" C LYS A 356 " ideal model delta sigma weight residual 111.71 119.00 -7.29 1.15e+00 7.56e-01 4.02e+01 ... (remaining 26401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10815 17.97 - 35.95: 689 35.95 - 53.92: 135 53.92 - 71.89: 34 71.89 - 89.86: 24 Dihedral angle restraints: 11697 sinusoidal: 4707 harmonic: 6990 Sorted by residual: dihedral pdb=" CA TRP H 94 " pdb=" C TRP H 94 " pdb=" N TRP H 96 " pdb=" CA TRP H 96 " ideal model delta harmonic sigma weight residual 180.00 122.70 57.30 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA TRP L 94 " pdb=" C TRP L 94 " pdb=" N TRP L 96 " pdb=" CA TRP L 96 " ideal model delta harmonic sigma weight residual 180.00 123.05 56.95 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ILE E 141 " pdb=" C ILE E 141 " pdb=" N ILE E 142 " pdb=" CA ILE E 142 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1717 0.078 - 0.155: 987 0.155 - 0.232: 182 0.232 - 0.310: 44 0.310 - 0.387: 7 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CA ARG A 166 " pdb=" N ARG A 166 " pdb=" C ARG A 166 " pdb=" CB ARG A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ALA J 532 " pdb=" N ALA J 532 " pdb=" C ALA J 532 " pdb=" CB ALA J 532 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ALA B 532 " pdb=" N ALA B 532 " pdb=" C ALA B 532 " pdb=" CB ALA B 532 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 2934 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP H 94 " 0.133 2.00e-02 2.50e+03 1.93e-01 3.74e+02 pdb=" C TRP H 94 " -0.329 2.00e-02 2.50e+03 pdb=" O TRP H 94 " 0.147 2.00e-02 2.50e+03 pdb=" N TRP H 96 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 94 " 0.131 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C TRP L 94 " -0.324 2.00e-02 2.50e+03 pdb=" O TRP L 94 " 0.144 2.00e-02 2.50e+03 pdb=" N TRP L 96 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 427 " -0.133 2.00e-02 2.50e+03 6.89e-02 1.19e+02 pdb=" CG TRP E 427 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP E 427 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP E 427 " 0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP E 427 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP E 427 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP E 427 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 427 " -0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 427 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 427 " -0.082 2.00e-02 2.50e+03 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 10446 3.02 - 3.49: 19002 3.49 - 3.96: 30398 3.96 - 4.43: 32778 4.43 - 4.90: 54776 Nonbonded interactions: 147400 Sorted by model distance: nonbonded pdb=" OE2 GLU I 62 " pdb=" OG1 THR I 77 " model vdw 2.555 3.040 nonbonded pdb=" OE2 GLU A 62 " pdb=" OG1 THR A 77 " model vdw 2.556 3.040 nonbonded pdb=" OE2 GLU E 62 " pdb=" OG1 THR E 77 " model vdw 2.556 3.040 nonbonded pdb=" OG1 THR K 19 " pdb=" OD1 ASP K 81 " model vdw 2.580 3.040 nonbonded pdb=" OE2 GLU I 83 " pdb=" OG SER I 243 " model vdw 2.582 3.040 ... (remaining 147395 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 No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.590 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.019 1.434 19500 Z= 1.191 Angle : 1.762 25.222 26490 Z= 1.165 Chirality : 0.094 0.387 2937 Planarity : 0.016 0.193 3378 Dihedral : 13.378 89.863 7083 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.99 % Favored : 92.34 % Rotamer: Outliers : 1.10 % Allowed : 2.62 % Favored : 96.29 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.09 (0.16), residues: 2375 helix: -0.07 (0.25), residues: 339 sheet: -0.31 (0.21), residues: 534 loop : -1.04 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 273 TYR 0.118 0.022 TYR F 586 PHE 0.099 0.013 PHE D 71 TRP 0.133 0.030 TRP E 427 HIS 0.016 0.004 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.01882 (19458) covalent geometry : angle 1.76286 (26406) SS BOND : bond 0.00720 ( 42) SS BOND : angle 1.51501 ( 84) hydrogen bonds : bond 0.14817 ( 553) hydrogen bonds : angle 7.34465 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 550 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8084 (m100) cc_final: 0.7853 (m-10) REVERT: A 178 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8407 (tmtt) REVERT: B 538 THR cc_start: 0.8702 (p) cc_final: 0.8494 (p) REVERT: B 575 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: C 75 MET cc_start: 0.7711 (mmm) cc_final: 0.7448 (mtp) REVERT: E 178 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8309 (tmtt) REVERT: E 396 MET cc_start: 0.8988 (pmm) cc_final: 0.7216 (mtt) REVERT: F 538 THR cc_start: 0.8745 (p) cc_final: 0.8481 (p) REVERT: F 575 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: G 18 MET cc_start: 0.8393 (ptt) cc_final: 0.8166 (ptp) REVERT: G 74 SER cc_start: 0.8763 (m) cc_final: 0.8560 (m) REVERT: G 75 MET cc_start: 0.7601 (mmm) cc_final: 0.7263 (mtp) REVERT: I 35 TRP cc_start: 0.8142 (m100) cc_final: 0.7725 (m-10) REVERT: I 315 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: I 396 MET cc_start: 0.8884 (pmm) cc_final: 0.7267 (mtt) REVERT: J 538 THR cc_start: 0.8857 (p) cc_final: 0.8530 (p) REVERT: J 575 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6213 (tt0) REVERT: J 647 GLU cc_start: 0.7417 (tt0) cc_final: 0.6881 (tt0) REVERT: K 75 MET cc_start: 0.7706 (mmm) cc_final: 0.7267 (mtp) REVERT: L 5 THR cc_start: 0.7812 (m) cc_final: 0.7478 (p) REVERT: L 46 LEU cc_start: 0.7935 (tp) cc_final: 0.7692 (pt) outliers start: 23 outliers final: 6 residues processed: 573 average time/residue: 0.1860 time to fit residues: 152.6433 Evaluate side-chains 348 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 338 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain J residue 575 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN A 262 ASN A 334 ASN A 425 ASN D 37 GLN D 38 HIS E 72 HIS E 105 HIS H 37 GLN H 38 HIS I 72 HIS I 334 ASN L 37 GLN L 38 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.162509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3382 r_free = 0.3382 target = 0.134968 restraints weight = 23804.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.134047 restraints weight = 25600.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133918 restraints weight = 26451.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133913 restraints weight = 25219.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133913 restraints weight = 24958.279| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19500 Z= 0.196 Angle : 0.794 12.502 26490 Z= 0.423 Chirality : 0.050 0.240 2937 Planarity : 0.005 0.046 3378 Dihedral : 7.877 89.888 2652 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.58 % Favored : 95.17 % Rotamer: Outliers : 3.43 % Allowed : 12.14 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.71 (0.16), residues: 2379 helix: 1.48 (0.28), residues: 363 sheet: -0.44 (0.19), residues: 660 loop : -1.03 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 3 TYR 0.024 0.002 TYR A 177 PHE 0.013 0.002 PHE A 383 TRP 0.028 0.002 TRP H 96 HIS 0.011 0.002 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00446 (19458) covalent geometry : angle 0.78563 (26406) SS BOND : bond 0.00485 ( 42) SS BOND : angle 2.17877 ( 84) hydrogen bonds : bond 0.04867 ( 553) hydrogen bonds : angle 5.49515 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 358 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8248 (m100) cc_final: 0.7931 (m100) REVERT: A 49 LYS cc_start: 0.8502 (mptt) cc_final: 0.8192 (mttp) REVERT: A 178 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8313 (tmtt) REVERT: A 396 MET cc_start: 0.8989 (pmm) cc_final: 0.7373 (mtt) REVERT: E 170 GLU cc_start: 0.7282 (tt0) cc_final: 0.6916 (mt-10) REVERT: E 396 MET cc_start: 0.8869 (pmm) cc_final: 0.7463 (mtt) REVERT: G 39 GLN cc_start: 0.7935 (tt0) cc_final: 0.7665 (tt0) REVERT: H 100 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8275 (mm-40) REVERT: I 35 TRP cc_start: 0.8282 (m100) cc_final: 0.7637 (m-10) REVERT: I 308 ARG cc_start: 0.7687 (mtp85) cc_final: 0.6867 (mmp-170) REVERT: I 396 MET cc_start: 0.8852 (pmm) cc_final: 0.7381 (mtt) outliers start: 72 outliers final: 43 residues processed: 401 average time/residue: 0.1574 time to fit residues: 95.6430 Evaluate side-chains 344 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 228 optimal weight: 0.0030 chunk 106 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 70 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.1130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN D 37 GLN E 72 HIS I 72 HIS I 105 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.162938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.147312 restraints weight = 23599.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135684 restraints weight = 33958.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.134425 restraints weight = 30195.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.134703 restraints weight = 29234.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.134908 restraints weight = 26557.842| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19500 Z= 0.149 Angle : 0.693 12.874 26490 Z= 0.369 Chirality : 0.046 0.212 2937 Planarity : 0.004 0.043 3378 Dihedral : 6.248 32.632 2640 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.30 % Favored : 94.45 % Rotamer: Outliers : 2.81 % Allowed : 14.33 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2379 helix: 1.54 (0.28), residues: 381 sheet: -0.52 (0.19), residues: 687 loop : -0.92 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 498 TYR 0.027 0.002 TYR E 482 PHE 0.012 0.002 PHE I 176 TRP 0.018 0.002 TRP E 35 HIS 0.009 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00327 (19458) covalent geometry : angle 0.68894 (26406) SS BOND : bond 0.00771 ( 42) SS BOND : angle 1.51856 ( 84) hydrogen bonds : bond 0.04000 ( 553) hydrogen bonds : angle 5.14356 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8217 (m100) cc_final: 0.7880 (m100) REVERT: A 49 LYS cc_start: 0.8451 (mptt) cc_final: 0.8196 (ptmm) REVERT: A 95 MET cc_start: 0.7558 (ptm) cc_final: 0.7287 (ptm) REVERT: A 178 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8216 (tmtt) REVERT: A 396 MET cc_start: 0.8918 (pmm) cc_final: 0.7374 (mtt) REVERT: A 498 ARG cc_start: 0.7031 (ttm110) cc_final: 0.6464 (tpt-90) REVERT: B 617 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.5610 (ttp-170) REVERT: C 25 SER cc_start: 0.8281 (p) cc_final: 0.8076 (m) REVERT: E 49 LYS cc_start: 0.8343 (mptt) cc_final: 0.8094 (mttp) REVERT: E 170 GLU cc_start: 0.7262 (tt0) cc_final: 0.7045 (mt-10) REVERT: E 275 GLU cc_start: 0.7819 (tp30) cc_final: 0.7606 (tp30) REVERT: E 396 MET cc_start: 0.8854 (pmm) cc_final: 0.7490 (mtt) REVERT: F 634 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7972 (mt-10) REVERT: G 39 GLN cc_start: 0.8008 (tt0) cc_final: 0.7766 (tt0) REVERT: I 35 TRP cc_start: 0.8206 (m100) cc_final: 0.7452 (m-10) REVERT: I 308 ARG cc_start: 0.7771 (mtp85) cc_final: 0.6885 (mmp-170) REVERT: I 396 MET cc_start: 0.8821 (pmm) cc_final: 0.7495 (mtt) REVERT: J 635 ILE cc_start: 0.8518 (mm) cc_final: 0.8213 (mm) outliers start: 59 outliers final: 40 residues processed: 384 average time/residue: 0.1537 time to fit residues: 90.0494 Evaluate side-chains 344 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 181 optimal weight: 0.0970 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 246 GLN E 72 HIS E 246 GLN E 300 ASN I 72 HIS I 246 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.165771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.139953 restraints weight = 23495.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.139305 restraints weight = 24094.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.139280 restraints weight = 25083.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.139279 restraints weight = 24534.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.139279 restraints weight = 24486.167| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19500 Z= 0.117 Angle : 0.636 12.474 26490 Z= 0.336 Chirality : 0.044 0.210 2937 Planarity : 0.004 0.049 3378 Dihedral : 5.772 29.473 2640 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.92 % Favored : 94.83 % Rotamer: Outliers : 3.19 % Allowed : 15.38 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.36 (0.17), residues: 2379 helix: 2.13 (0.28), residues: 363 sheet: -0.38 (0.19), residues: 702 loop : -0.82 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 45 TYR 0.021 0.001 TYR H 91 PHE 0.010 0.001 PHE H 71 TRP 0.036 0.001 TRP E 35 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00252 (19458) covalent geometry : angle 0.63249 (26406) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.40448 ( 84) hydrogen bonds : bond 0.03466 ( 553) hydrogen bonds : angle 4.90149 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 330 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8238 (m100) cc_final: 0.7941 (m100) REVERT: A 95 MET cc_start: 0.7403 (ptm) cc_final: 0.7160 (ptm) REVERT: A 178 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8205 (mtmm) REVERT: A 396 MET cc_start: 0.8790 (pmm) cc_final: 0.7427 (mtt) REVERT: B 617 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.5733 (ttp-170) REVERT: C 25 SER cc_start: 0.8304 (p) cc_final: 0.8030 (m) REVERT: E 67 ASN cc_start: 0.8017 (t0) cc_final: 0.7558 (t0) REVERT: E 122 LEU cc_start: 0.8068 (mm) cc_final: 0.7809 (mt) REVERT: E 170 GLU cc_start: 0.7185 (tt0) cc_final: 0.6981 (mt-10) REVERT: E 207 LYS cc_start: 0.7862 (ptmm) cc_final: 0.7621 (ptmm) REVERT: E 275 GLU cc_start: 0.7585 (tp30) cc_final: 0.7328 (tp30) REVERT: E 396 MET cc_start: 0.8811 (pmm) cc_final: 0.7565 (mtt) REVERT: E 427 TRP cc_start: 0.8842 (m100) cc_final: 0.8547 (m100) REVERT: G 39 GLN cc_start: 0.8032 (tt0) cc_final: 0.7761 (tt0) REVERT: I 95 MET cc_start: 0.6942 (ptm) cc_final: 0.6703 (ptm) REVERT: I 114 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7131 (mt0) REVERT: I 208 LEU cc_start: 0.7323 (mp) cc_final: 0.7080 (mt) REVERT: I 308 ARG cc_start: 0.7700 (mtp85) cc_final: 0.6913 (mmp-170) REVERT: I 396 MET cc_start: 0.8758 (pmm) cc_final: 0.7566 (mtt) REVERT: J 635 ILE cc_start: 0.8421 (mm) cc_final: 0.8118 (mm) REVERT: K 39 GLN cc_start: 0.7931 (tt0) cc_final: 0.7690 (tt0) outliers start: 67 outliers final: 38 residues processed: 373 average time/residue: 0.1569 time to fit residues: 89.1186 Evaluate side-chains 329 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 59 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 195 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 658 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.161435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137591 restraints weight = 23987.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.135400 restraints weight = 37751.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136249 restraints weight = 36131.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.135166 restraints weight = 27452.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.135570 restraints weight = 25605.528| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19500 Z= 0.158 Angle : 0.635 12.639 26490 Z= 0.337 Chirality : 0.045 0.195 2937 Planarity : 0.004 0.050 3378 Dihedral : 5.571 27.343 2638 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 3.10 % Allowed : 17.00 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.36 (0.17), residues: 2379 helix: 2.10 (0.28), residues: 360 sheet: -0.38 (0.19), residues: 732 loop : -0.81 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.019 0.002 TYR H 91 PHE 0.011 0.002 PHE F 522 TRP 0.043 0.001 TRP E 35 HIS 0.007 0.002 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00368 (19458) covalent geometry : angle 0.63103 (26406) SS BOND : bond 0.00446 ( 42) SS BOND : angle 1.45104 ( 84) hydrogen bonds : bond 0.03578 ( 553) hydrogen bonds : angle 4.91458 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8220 (m100) cc_final: 0.7999 (m100) REVERT: A 49 LYS cc_start: 0.8277 (mptt) cc_final: 0.8038 (ptmm) REVERT: A 95 MET cc_start: 0.7441 (ptm) cc_final: 0.7233 (ptm) REVERT: A 114 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7221 (mt0) REVERT: A 246 GLN cc_start: 0.6826 (mp10) cc_final: 0.6586 (tp-100) REVERT: A 396 MET cc_start: 0.8769 (pmm) cc_final: 0.7460 (mtt) REVERT: B 617 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.5759 (ttp-170) REVERT: E 114 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7322 (mp10) REVERT: E 122 LEU cc_start: 0.8109 (mm) cc_final: 0.7834 (mt) REVERT: E 207 LYS cc_start: 0.8011 (ptmm) cc_final: 0.7802 (ptmm) REVERT: E 275 GLU cc_start: 0.7727 (tp30) cc_final: 0.7246 (tp30) REVERT: E 396 MET cc_start: 0.8734 (pmm) cc_final: 0.7553 (mtt) REVERT: E 427 TRP cc_start: 0.8890 (m100) cc_final: 0.8621 (m100) REVERT: F 617 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.5545 (ttp-170) REVERT: F 628 TRP cc_start: 0.8038 (m100) cc_final: 0.7830 (m100) REVERT: G 39 GLN cc_start: 0.8134 (tt0) cc_final: 0.7870 (tt0) REVERT: I 95 MET cc_start: 0.7079 (ptm) cc_final: 0.6774 (ptm) REVERT: I 114 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7238 (mt0) REVERT: I 308 ARG cc_start: 0.7737 (mtp85) cc_final: 0.6995 (mmp-170) REVERT: I 396 MET cc_start: 0.8805 (pmm) cc_final: 0.7634 (mtt) REVERT: J 540 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7269 (tm-30) REVERT: J 617 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.5554 (ttp-170) REVERT: J 635 ILE cc_start: 0.8526 (mm) cc_final: 0.8206 (mm) REVERT: K 39 GLN cc_start: 0.8053 (tt0) cc_final: 0.7772 (tt0) outliers start: 65 outliers final: 48 residues processed: 356 average time/residue: 0.1564 time to fit residues: 84.7541 Evaluate side-chains 352 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 166 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN C 6 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.163439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.139850 restraints weight = 23547.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136893 restraints weight = 39219.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.135957 restraints weight = 39789.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.133386 restraints weight = 33043.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.134172 restraints weight = 29874.180| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19500 Z= 0.115 Angle : 0.603 12.513 26490 Z= 0.319 Chirality : 0.044 0.201 2937 Planarity : 0.004 0.060 3378 Dihedral : 5.381 29.356 2637 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 2.71 % Allowed : 18.05 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.22 (0.17), residues: 2379 helix: 2.24 (0.29), residues: 360 sheet: -0.26 (0.19), residues: 720 loop : -0.75 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 542 TYR 0.019 0.001 TYR H 91 PHE 0.009 0.001 PHE H 71 TRP 0.034 0.001 TRP E 35 HIS 0.008 0.001 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00256 (19458) covalent geometry : angle 0.59948 (26406) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.35365 ( 84) hydrogen bonds : bond 0.03291 ( 553) hydrogen bonds : angle 4.86347 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8241 (m100) cc_final: 0.7952 (m100) REVERT: A 114 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7348 (mt0) REVERT: A 145 MET cc_start: 0.7499 (mtp) cc_final: 0.7289 (mtt) REVERT: A 246 GLN cc_start: 0.6882 (mp10) cc_final: 0.6636 (tp-100) REVERT: A 396 MET cc_start: 0.8715 (pmm) cc_final: 0.7451 (mtt) REVERT: B 617 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.5765 (ttp-170) REVERT: E 50 THR cc_start: 0.8446 (t) cc_final: 0.8190 (m) REVERT: E 114 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7054 (mt0) REVERT: E 198 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8685 (t) REVERT: E 207 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7778 (ptmm) REVERT: E 275 GLU cc_start: 0.7707 (tp30) cc_final: 0.7197 (tp30) REVERT: E 396 MET cc_start: 0.8731 (pmm) cc_final: 0.7551 (mtt) REVERT: E 427 TRP cc_start: 0.8886 (m100) cc_final: 0.8644 (m100) REVERT: F 617 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.5464 (ttp-170) REVERT: G 39 GLN cc_start: 0.8160 (tt0) cc_final: 0.7891 (tt0) REVERT: I 35 TRP cc_start: 0.8152 (m100) cc_final: 0.7462 (m-10) REVERT: I 95 MET cc_start: 0.6963 (ptm) cc_final: 0.6657 (ptm) REVERT: I 114 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7250 (mt0) REVERT: I 308 ARG cc_start: 0.7771 (mtp85) cc_final: 0.6984 (mmp-170) REVERT: I 396 MET cc_start: 0.8816 (pmm) cc_final: 0.7609 (mtt) REVERT: J 617 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.5461 (ttp-170) REVERT: J 635 ILE cc_start: 0.8405 (mm) cc_final: 0.8119 (mm) REVERT: K 6 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: K 39 GLN cc_start: 0.8123 (tt0) cc_final: 0.7822 (tt0) outliers start: 57 outliers final: 40 residues processed: 348 average time/residue: 0.1536 time to fit residues: 81.8069 Evaluate side-chains 345 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 17 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 29 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 195 ASN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.134690 restraints weight = 24337.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.133360 restraints weight = 37619.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.132096 restraints weight = 42319.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130859 restraints weight = 38785.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.127102 restraints weight = 37338.309| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19500 Z= 0.279 Angle : 0.745 12.856 26490 Z= 0.392 Chirality : 0.049 0.231 2937 Planarity : 0.005 0.066 3378 Dihedral : 5.715 28.380 2637 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 3.81 % Allowed : 17.71 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.60 (0.17), residues: 2379 helix: 1.62 (0.28), residues: 363 sheet: -0.47 (0.19), residues: 714 loop : -0.91 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 64 TYR 0.025 0.003 TYR K 50 PHE 0.019 0.002 PHE E 361 TRP 0.039 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00666 (19458) covalent geometry : angle 0.74168 (26406) SS BOND : bond 0.00478 ( 42) SS BOND : angle 1.50592 ( 84) hydrogen bonds : bond 0.04156 ( 553) hydrogen bonds : angle 5.20234 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8310 (m100) cc_final: 0.7630 (m-10) REVERT: A 49 LYS cc_start: 0.8544 (mptt) cc_final: 0.8002 (ptmm) REVERT: A 114 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7390 (mt0) REVERT: A 145 MET cc_start: 0.7937 (mtp) cc_final: 0.7730 (mtt) REVERT: A 180 ASP cc_start: 0.8750 (t0) cc_final: 0.8256 (t0) REVERT: A 246 GLN cc_start: 0.7320 (mp10) cc_final: 0.6843 (tp-100) REVERT: A 396 MET cc_start: 0.8603 (pmm) cc_final: 0.7331 (mtt) REVERT: A 423 ILE cc_start: 0.8837 (mp) cc_final: 0.8477 (mp) REVERT: B 617 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.5522 (ttp-170) REVERT: D 90 GLN cc_start: 0.9437 (pp30) cc_final: 0.9158 (pp30) REVERT: E 114 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7040 (mt0) REVERT: E 198 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8827 (t) REVERT: E 207 LYS cc_start: 0.8355 (ptmm) cc_final: 0.8100 (ptmm) REVERT: E 275 GLU cc_start: 0.8256 (tp30) cc_final: 0.7430 (tp30) REVERT: E 396 MET cc_start: 0.8798 (pmm) cc_final: 0.7507 (mtt) REVERT: F 617 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.4425 (ttp-170) REVERT: F 628 TRP cc_start: 0.8191 (m100) cc_final: 0.7930 (m100) REVERT: F 630 GLN cc_start: 0.8763 (mp10) cc_final: 0.8462 (mt0) REVERT: G 39 GLN cc_start: 0.8310 (tt0) cc_final: 0.7925 (tt0) REVERT: G 46 GLU cc_start: 0.7299 (tt0) cc_final: 0.7040 (mt-10) REVERT: H 90 GLN cc_start: 0.9397 (pp30) cc_final: 0.9055 (pp30) REVERT: I 114 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7291 (mt0) REVERT: I 246 GLN cc_start: 0.7296 (mp10) cc_final: 0.6941 (tp-100) REVERT: I 396 MET cc_start: 0.8864 (pmm) cc_final: 0.7468 (mtt) REVERT: J 540 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7325 (tm-30) REVERT: J 617 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.5430 (ttp-170) REVERT: J 630 GLN cc_start: 0.8804 (mp10) cc_final: 0.8562 (mt0) REVERT: K 39 GLN cc_start: 0.8408 (tt0) cc_final: 0.8119 (tt0) REVERT: L 90 GLN cc_start: 0.9430 (pp30) cc_final: 0.9074 (pp30) outliers start: 80 outliers final: 60 residues processed: 368 average time/residue: 0.1523 time to fit residues: 85.9996 Evaluate side-chains 372 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.138860 restraints weight = 23967.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137715 restraints weight = 37050.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.130953 restraints weight = 38965.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.129208 restraints weight = 27743.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.129368 restraints weight = 25095.000| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19500 Z= 0.156 Angle : 0.637 12.609 26490 Z= 0.336 Chirality : 0.045 0.209 2937 Planarity : 0.004 0.054 3378 Dihedral : 5.492 29.381 2637 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 3.14 % Allowed : 18.90 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.50 (0.17), residues: 2379 helix: 1.91 (0.28), residues: 363 sheet: -0.41 (0.19), residues: 714 loop : -0.91 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 542 TYR 0.016 0.002 TYR G 50 PHE 0.011 0.001 PHE E 361 TRP 0.046 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00363 (19458) covalent geometry : angle 0.63332 (26406) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.40129 ( 84) hydrogen bonds : bond 0.03484 ( 553) hydrogen bonds : angle 5.03310 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 316 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8234 (m100) cc_final: 0.7516 (m-10) REVERT: A 49 LYS cc_start: 0.8343 (mptt) cc_final: 0.8045 (ptmm) REVERT: A 114 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7219 (mt0) REVERT: A 145 MET cc_start: 0.7859 (mtp) cc_final: 0.7620 (mtt) REVERT: A 180 ASP cc_start: 0.8843 (t0) cc_final: 0.8298 (t0) REVERT: A 246 GLN cc_start: 0.7264 (mp10) cc_final: 0.6795 (tp-100) REVERT: A 396 MET cc_start: 0.8532 (pmm) cc_final: 0.7304 (mtt) REVERT: A 423 ILE cc_start: 0.8804 (mp) cc_final: 0.8430 (mp) REVERT: B 617 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.5438 (ttp-170) REVERT: D 90 GLN cc_start: 0.9378 (pp30) cc_final: 0.9126 (pp30) REVERT: E 114 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7063 (mt0) REVERT: E 198 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8789 (t) REVERT: E 275 GLU cc_start: 0.8000 (tp30) cc_final: 0.7574 (tp30) REVERT: E 396 MET cc_start: 0.8784 (pmm) cc_final: 0.7467 (mtt) REVERT: F 617 ARG cc_start: 0.7400 (mmt-90) cc_final: 0.5129 (ttp-170) REVERT: G 39 GLN cc_start: 0.8318 (tt0) cc_final: 0.7887 (tt0) REVERT: H 90 GLN cc_start: 0.9363 (pp30) cc_final: 0.8863 (pp30) REVERT: I 50 THR cc_start: 0.8491 (t) cc_final: 0.8220 (m) REVERT: I 114 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7305 (mt0) REVERT: I 246 GLN cc_start: 0.7220 (mp10) cc_final: 0.6898 (tp-100) REVERT: I 396 MET cc_start: 0.8843 (pmm) cc_final: 0.7455 (mtt) REVERT: I 458 TYR cc_start: 0.8384 (t80) cc_final: 0.8107 (t80) REVERT: J 540 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7378 (tm-30) REVERT: J 617 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.5395 (ttp-170) REVERT: K 6 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: K 39 GLN cc_start: 0.8389 (tt0) cc_final: 0.8101 (tt0) REVERT: L 32 ASN cc_start: 0.8665 (m-40) cc_final: 0.8411 (m110) REVERT: L 90 GLN cc_start: 0.9388 (pp30) cc_final: 0.9043 (pp30) outliers start: 66 outliers final: 58 residues processed: 350 average time/residue: 0.1489 time to fit residues: 80.5887 Evaluate side-chains 360 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 45 PHE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 46 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 630 GLN K 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.159489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139588 restraints weight = 23871.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.137911 restraints weight = 35661.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.138204 restraints weight = 37523.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137162 restraints weight = 30284.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.135451 restraints weight = 35427.550| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19500 Z= 0.150 Angle : 0.638 12.498 26490 Z= 0.333 Chirality : 0.045 0.212 2937 Planarity : 0.004 0.049 3378 Dihedral : 5.405 29.227 2637 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 2.90 % Allowed : 19.43 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.47 (0.17), residues: 2379 helix: 1.95 (0.28), residues: 363 sheet: -0.29 (0.20), residues: 678 loop : -0.96 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 542 TYR 0.015 0.002 TYR K 50 PHE 0.011 0.001 PHE E 361 TRP 0.057 0.002 TRP E 35 HIS 0.010 0.001 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00354 (19458) covalent geometry : angle 0.63479 (26406) SS BOND : bond 0.00413 ( 42) SS BOND : angle 1.31985 ( 84) hydrogen bonds : bond 0.03452 ( 553) hydrogen bonds : angle 5.00532 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8204 (m100) cc_final: 0.7678 (m-10) REVERT: A 49 LYS cc_start: 0.8311 (mptt) cc_final: 0.8075 (ptmm) REVERT: A 180 ASP cc_start: 0.8804 (t0) cc_final: 0.8234 (t0) REVERT: A 246 GLN cc_start: 0.7155 (mp10) cc_final: 0.6808 (tp-100) REVERT: A 396 MET cc_start: 0.8543 (pmm) cc_final: 0.7575 (mtt) REVERT: A 423 ILE cc_start: 0.8783 (mp) cc_final: 0.8362 (mp) REVERT: B 617 ARG cc_start: 0.8399 (mmt-90) cc_final: 0.5675 (ttp-170) REVERT: D 90 GLN cc_start: 0.9386 (pp30) cc_final: 0.9183 (pp30) REVERT: E 198 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8670 (t) REVERT: E 246 GLN cc_start: 0.7027 (mp10) cc_final: 0.6787 (tp-100) REVERT: E 275 GLU cc_start: 0.7842 (tp30) cc_final: 0.7499 (tp30) REVERT: E 396 MET cc_start: 0.8669 (pmm) cc_final: 0.7701 (mtt) REVERT: F 617 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.5467 (ttp-110) REVERT: G 39 GLN cc_start: 0.8239 (tt0) cc_final: 0.7840 (tt0) REVERT: G 71 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7647 (pmt-80) REVERT: H 90 GLN cc_start: 0.9356 (pp30) cc_final: 0.8929 (pp30) REVERT: I 35 TRP cc_start: 0.8134 (m100) cc_final: 0.7405 (m-10) REVERT: I 50 THR cc_start: 0.8448 (t) cc_final: 0.8181 (m) REVERT: I 114 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7450 (mt0) REVERT: I 396 MET cc_start: 0.8737 (pmm) cc_final: 0.7599 (mtt) REVERT: J 540 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7373 (tm-30) REVERT: J 617 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.4923 (ttp-170) REVERT: K 39 GLN cc_start: 0.8289 (tt0) cc_final: 0.8002 (tt0) REVERT: L 90 GLN cc_start: 0.9381 (pp30) cc_final: 0.9076 (pp30) outliers start: 61 outliers final: 52 residues processed: 340 average time/residue: 0.1553 time to fit residues: 80.7411 Evaluate side-chains 350 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 0 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 246 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 630 GLN L 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.161543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.139926 restraints weight = 23871.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.137970 restraints weight = 39648.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131668 restraints weight = 40072.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.129988 restraints weight = 31270.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.130961 restraints weight = 28556.950| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19500 Z= 0.127 Angle : 0.617 12.266 26490 Z= 0.321 Chirality : 0.044 0.204 2937 Planarity : 0.004 0.049 3378 Dihedral : 5.240 28.189 2637 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.81 % Allowed : 19.71 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.34 (0.17), residues: 2379 helix: 2.15 (0.29), residues: 363 sheet: -0.20 (0.20), residues: 654 loop : -0.90 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 542 TYR 0.019 0.002 TYR G 7 PHE 0.010 0.001 PHE J 522 TRP 0.053 0.001 TRP E 35 HIS 0.010 0.001 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00293 (19458) covalent geometry : angle 0.61382 (26406) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.24291 ( 84) hydrogen bonds : bond 0.03209 ( 553) hydrogen bonds : angle 4.94958 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8213 (m100) cc_final: 0.7451 (m-10) REVERT: A 49 LYS cc_start: 0.8292 (mptt) cc_final: 0.7998 (ptmm) REVERT: A 180 ASP cc_start: 0.8789 (t0) cc_final: 0.8170 (t0) REVERT: A 246 GLN cc_start: 0.7248 (mp10) cc_final: 0.6780 (tp-100) REVERT: A 396 MET cc_start: 0.8443 (pmm) cc_final: 0.7345 (mtt) REVERT: A 423 ILE cc_start: 0.8735 (mp) cc_final: 0.8339 (mp) REVERT: A 443 ILE cc_start: 0.8249 (tp) cc_final: 0.7989 (mm) REVERT: B 617 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.5491 (ttp-170) REVERT: D 90 GLN cc_start: 0.9364 (pp30) cc_final: 0.9008 (pp30) REVERT: E 198 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8772 (t) REVERT: E 246 GLN cc_start: 0.7183 (mp10) cc_final: 0.6749 (tp-100) REVERT: E 275 GLU cc_start: 0.7888 (tp30) cc_final: 0.7497 (tp30) REVERT: E 396 MET cc_start: 0.8733 (pmm) cc_final: 0.7514 (mtt) REVERT: F 617 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.5177 (ttp-170) REVERT: G 39 GLN cc_start: 0.8341 (tt0) cc_final: 0.7887 (tt0) REVERT: G 100 LEU cc_start: 0.8188 (mt) cc_final: 0.7515 (mt) REVERT: H 90 GLN cc_start: 0.9359 (pp30) cc_final: 0.8906 (pp30) REVERT: I 35 TRP cc_start: 0.8152 (m100) cc_final: 0.7172 (m-10) REVERT: I 114 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7211 (mt0) REVERT: I 178 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7882 (mtmm) REVERT: I 396 MET cc_start: 0.8820 (pmm) cc_final: 0.7472 (mtt) REVERT: J 540 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7305 (tm-30) REVERT: J 617 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.5094 (ttp-170) REVERT: J 635 ILE cc_start: 0.8241 (mm) cc_final: 0.7946 (mm) REVERT: K 39 GLN cc_start: 0.8374 (tt0) cc_final: 0.8072 (tt0) REVERT: L 32 ASN cc_start: 0.8468 (m110) cc_final: 0.8260 (m110) REVERT: L 90 GLN cc_start: 0.9352 (pp30) cc_final: 0.8927 (pp30) outliers start: 59 outliers final: 51 residues processed: 343 average time/residue: 0.1567 time to fit residues: 82.1420 Evaluate side-chains 345 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 271 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139464 restraints weight = 24094.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.137662 restraints weight = 39918.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135946 restraints weight = 41811.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.134365 restraints weight = 41510.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134891 restraints weight = 36960.003| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19500 Z= 0.161 Angle : 0.639 12.472 26490 Z= 0.332 Chirality : 0.045 0.263 2937 Planarity : 0.004 0.050 3378 Dihedral : 5.258 28.044 2637 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 2.90 % Allowed : 19.62 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.41 (0.17), residues: 2379 helix: 2.07 (0.28), residues: 363 sheet: -0.33 (0.20), residues: 684 loop : -0.90 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 542 TYR 0.023 0.002 TYR G 7 PHE 0.012 0.002 PHE E 361 TRP 0.058 0.002 TRP E 35 HIS 0.011 0.002 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00378 (19458) covalent geometry : angle 0.63574 (26406) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.24661 ( 84) hydrogen bonds : bond 0.03390 ( 553) hydrogen bonds : angle 4.99834 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.06 seconds wall clock time: 56 minutes 20.51 seconds (3380.51 seconds total)