Starting phenix.real_space_refine on Fri Jan 16 13:57:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7c_13235/01_2026/7p7c_13235.map" } resolution = 2.4 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= 0.005 sd= 0.023 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 11 5.49 5 S 266 5.16 5 C 24345 2.51 5 N 6163 2.21 5 O 7502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38320 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7013 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4735 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2438 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4559 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 578} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3602 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1218 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 151 Unusual residues: {'3PE': 2, 'LFA': 1, 'UQ8': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UQ8:plan-2': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 328 Classifications: {'water': 328} Link IDs: {None: 327} Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "M" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "N" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 77.233 60.505 195.305 1.00 16.35 S ATOM 2741 SG CYS F 357 80.779 60.158 199.592 1.00 17.33 S ATOM 3062 SG CYS F 398 75.055 56.791 200.421 1.00 19.81 S ATOM 2697 SG CYS F 351 79.307 54.169 196.715 1.00 15.71 S ATOM 4054 SG CYS E 92 88.930 52.847 216.072 1.00 30.58 S ATOM 4088 SG CYS E 97 89.252 53.619 219.567 1.00 26.81 S ATOM 4366 SG CYS E 133 83.700 52.248 216.045 1.00 34.67 S ATOM 4392 SG CYS E 137 83.116 53.079 219.328 1.00 37.49 S ATOM 5476 SG CYS G 114 86.906 65.900 177.016 1.00 22.99 S ATOM 5416 SG CYS G 105 92.243 69.749 178.144 1.00 16.30 S ATOM 5436 SG CYS G 108 92.780 63.616 176.144 1.00 16.21 S ATOM 5830 SG CYS G 156 81.331 58.312 182.572 1.00 18.34 S ATOM 5811 SG CYS G 153 87.315 57.199 185.370 1.00 10.94 S ATOM 5859 SG CYS G 159 84.234 52.556 182.113 1.00 16.79 S ATOM 6203 SG CYS G 203 86.225 57.614 178.721 1.00 14.72 S ATOM 6428 SG CYS G 230 81.722 48.320 158.095 1.00 15.64 S ATOM 6713 SG CYS G 265 81.878 44.748 163.573 1.00 20.34 S ATOM 6476 SG CYS G 237 76.580 48.205 161.541 1.00 21.56 S ATOM 6452 SG CYS G 233 78.552 42.683 158.481 1.00 21.77 S ATOM 4877 SG CYS G 36 75.007 59.301 185.582 1.00 18.75 S ATOM 4953 SG CYS G 47 76.662 62.740 185.745 1.00 11.21 S ATOM 4979 SG CYS G 50 70.987 64.445 185.829 1.00 10.08 S ATOM 5128 SG CYS G 69 70.376 60.829 185.604 1.00 14.77 S ATOM 17221 SG CYS B 129 96.078 92.140 151.683 1.00 19.09 S ATOM 16718 SG CYS B 64 101.456 95.898 152.865 1.00 21.95 S ATOM 16712 SG CYS B 63 96.035 98.087 154.980 1.00 23.91 S ATOM 17438 SG CYS B 158 98.263 92.260 157.297 1.00 24.82 S ATOM 18769 SG CYS I 102 97.211 86.673 163.686 1.00 14.91 S ATOM 18744 SG CYS I 99 102.508 85.195 159.815 1.00 14.88 S ATOM 18787 SG CYS I 105 101.330 82.153 165.441 1.00 20.20 S ATOM 18502 SG CYS I 70 97.191 81.255 160.480 1.00 13.55 S ATOM 18816 SG CYS I 109 102.604 76.919 171.862 1.00 16.75 S ATOM 18479 SG CYS I 66 100.291 75.985 165.904 1.00 14.35 S ATOM 18439 SG CYS I 60 104.576 71.741 168.119 1.00 22.02 S ATOM 18457 SG CYS I 63 98.431 72.428 170.938 1.00 16.13 S Time building chain proxies: 7.82, per 1000 atoms: 0.20 Number of scatterers: 38320 At special positions: 0 Unit cell: (158, 212, 247.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 266 16.00 P 11 15.00 O 7502 8.00 N 6163 7.00 C 24345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8614 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.777A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.573A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.008A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.123A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.927A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.740A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.992A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.750A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.928A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.722A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.455A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.217A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.894A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.445A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.448A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.535A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.205A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.969A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1716 hydrogen bonds defined for protein. 5148 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: 6.41 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15894 1.42 - 1.64: 21908 1.64 - 1.86: 407 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38301 Sorted by residual: bond pdb=" CG PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 1.503 1.222 0.281 3.40e-02 8.65e+02 6.83e+01 bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C ILE H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.372 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.608 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 38296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 51508 3.51 - 7.01: 369 7.01 - 10.52: 53 10.52 - 14.03: 12 14.03 - 17.54: 3 Bond angle restraints: 51945 Sorted by residual: angle pdb=" N PRO N 5 " pdb=" CD PRO N 5 " pdb=" CG PRO N 5 " ideal model delta sigma weight residual 103.20 87.75 15.45 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO N 5 " pdb=" N PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA PRO N 5 " pdb=" CB PRO N 5 " pdb=" CG PRO N 5 " ideal model delta sigma weight residual 104.50 94.45 10.05 1.90e+00 2.77e-01 2.80e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 98.42 11.39 2.21e+00 2.05e-01 2.66e+01 angle pdb=" CA LEU L 511 " pdb=" CB LEU L 511 " pdb=" CG LEU L 511 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 ... (remaining 51940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 20738 22.93 - 45.86: 1501 45.86 - 68.79: 250 68.79 - 91.72: 57 91.72 - 114.65: 7 Dihedral angle restraints: 22553 sinusoidal: 9084 harmonic: 13469 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 131.38 48.62 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 144.72 35.28 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.04 34.96 0 5.00e+00 4.00e-02 4.89e+01 ... (remaining 22550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5765 4.240 - 8.479: 0 8.479 - 12.719: 0 12.719 - 16.959: 0 16.959 - 21.198: 28 Chirality restraints: 5793 Sorted by residual: chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5790 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 H 402 " -0.022 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" C1M UQ8 H 402 " -0.075 2.00e-02 2.50e+03 pdb=" C2 UQ8 H 402 " 0.021 2.00e-02 2.50e+03 pdb=" C3 UQ8 H 402 " 0.001 2.00e-02 2.50e+03 pdb=" C4 UQ8 H 402 " -0.005 2.00e-02 2.50e+03 pdb=" C5 UQ8 H 402 " 0.016 2.00e-02 2.50e+03 pdb=" C6 UQ8 H 402 " 0.002 2.00e-02 2.50e+03 pdb=" C7 UQ8 H 402 " -0.001 2.00e-02 2.50e+03 pdb=" O2 UQ8 H 402 " 0.075 2.00e-02 2.50e+03 pdb=" O3 UQ8 H 402 " -0.001 2.00e-02 2.50e+03 pdb=" O4 UQ8 H 402 " -0.088 2.00e-02 2.50e+03 pdb=" O5 UQ8 H 402 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO N 65 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" C VAL N 63 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.018 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.016 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2386 2.73 - 3.27: 38652 3.27 - 3.81: 73212 3.81 - 4.36: 91208 4.36 - 4.90: 146781 Nonbonded interactions: 352239 Sorted by model distance: nonbonded pdb=" O GLY A 96 " pdb=" O HOH A 201 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP K 57 " pdb=" OH TYR J 137 " model vdw 2.207 3.040 nonbonded pdb=" OG SER L 37 " pdb=" OD1 ASN L 121 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.245 3.040 nonbonded pdb=" OG SER L 150 " pdb=" O HOH L 901 " model vdw 2.247 3.040 ... (remaining 352234 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.510 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 36.380 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 38337 Z= 0.245 Angle : 0.837 17.537 52038 Z= 0.420 Chirality : 1.471 21.198 5793 Planarity : 0.006 0.088 6491 Dihedral : 16.232 114.653 13939 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 1.61 % Allowed : 16.10 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.11), residues: 4675 helix: 0.52 (0.09), residues: 2666 sheet: -0.33 (0.29), residues: 319 loop : -0.73 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 859 TYR 0.032 0.002 TYR N 260 PHE 0.042 0.002 PHE H 196 TRP 0.042 0.002 TRP H 260 HIS 0.022 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.00538 (38301) covalent geometry : angle 0.81841 (51945) hydrogen bonds : bond 0.06856 ( 1716) hydrogen bonds : angle 4.86366 ( 5148) metal coordination : bond 0.05418 ( 36) metal coordination : angle 4.19918 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 537 time to evaluate : 1.605 Fit side-chains REVERT: F 78 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7780 (mppt) REVERT: G 625 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8218 (p0) REVERT: G 834 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: B 39 MET cc_start: 0.7763 (tmm) cc_final: 0.7503 (tmm) REVERT: H 238 PHE cc_start: 0.7816 (m-10) cc_final: 0.7440 (m-80) REVERT: H 277 PHE cc_start: 0.7531 (m-80) cc_final: 0.7295 (m-80) REVERT: H 280 MET cc_start: 0.6641 (mmt) cc_final: 0.6386 (ptp) REVERT: L 430 PHE cc_start: 0.5991 (m-10) cc_final: 0.5536 (m-80) REVERT: M 407 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8323 (tp30) outliers start: 62 outliers final: 42 residues processed: 592 average time/residue: 0.7469 time to fit residues: 533.3091 Evaluate side-chains 534 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 490 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 497 SER Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain J residue 23 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.0370 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 3.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 400 HIS E 46 GLN G 232 GLN C 16 GLN C 224 HIS ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 435 HIS K 5 GLN K 88 GLN J 22 HIS J 86 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081686 restraints weight = 40976.219| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.06 r_work: 0.3106 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.255 38337 Z= 0.396 Angle : 2.499 55.943 52038 Z= 1.436 Chirality : 0.443 6.529 5793 Planarity : 0.004 0.073 6491 Dihedral : 9.504 114.641 5702 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 2.99 % Allowed : 14.44 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 4675 helix: 1.23 (0.10), residues: 2668 sheet: -0.12 (0.29), residues: 318 loop : -0.51 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 374 TYR 0.037 0.002 TYR N 260 PHE 0.032 0.001 PHE N 72 TRP 0.019 0.001 TRP H 260 HIS 0.010 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01148 (38301) covalent geometry : angle 2.17786 (51945) hydrogen bonds : bond 0.05585 ( 1716) hydrogen bonds : angle 4.37604 ( 5148) metal coordination : bond 0.04286 ( 36) metal coordination : angle 29.05931 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 529 time to evaluate : 1.590 Fit side-chains REVERT: F 78 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7843 (mppt) REVERT: G 252 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: G 834 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: C 400 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8046 (mp10) REVERT: H 44 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: H 68 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7130 (t80) REVERT: H 164 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7045 (mp) REVERT: H 238 PHE cc_start: 0.7429 (m-10) cc_final: 0.7119 (m-80) REVERT: H 277 PHE cc_start: 0.7145 (m-80) cc_final: 0.6662 (m-80) REVERT: H 281 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.5523 (mpp) REVERT: H 293 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7371 (ttp-110) REVERT: L 178 ASP cc_start: 0.7805 (m-30) cc_final: 0.7569 (m-30) REVERT: L 430 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5043 (m-80) REVERT: N 455 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5343 (mp) outliers start: 115 outliers final: 31 residues processed: 607 average time/residue: 0.7541 time to fit residues: 552.1264 Evaluate side-chains 534 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 494 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 281 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 85 optimal weight: 2.9990 chunk 368 optimal weight: 0.7980 chunk 312 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 462 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 46 GLN G 54 GLN G 768 ASN G 828 GLN C 16 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS M 159 HIS N 149 GLN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079754 restraints weight = 40568.155| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.06 r_work: 0.3064 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38337 Z= 0.399 Angle : 2.495 52.736 52038 Z= 1.435 Chirality : 0.448 6.579 5793 Planarity : 0.004 0.076 6491 Dihedral : 9.199 114.630 5659 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 2.91 % Allowed : 14.70 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4675 helix: 1.42 (0.10), residues: 2683 sheet: -0.12 (0.30), residues: 316 loop : -0.37 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 562 TYR 0.028 0.002 TYR N 260 PHE 0.031 0.002 PHE N 72 TRP 0.016 0.001 TRP H 260 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01143 (38301) covalent geometry : angle 2.17920 (51945) hydrogen bonds : bond 0.06009 ( 1716) hydrogen bonds : angle 4.38906 ( 5148) metal coordination : bond 0.05045 ( 36) metal coordination : angle 28.82909 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 506 time to evaluate : 1.708 Fit side-chains REVERT: F 78 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7848 (mppt) REVERT: F 95 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: G 806 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: H 44 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: H 164 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7098 (mp) REVERT: H 238 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: H 281 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.5697 (mpp) REVERT: H 293 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7391 (ttp-110) REVERT: H 295 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7470 (OUTLIER) REVERT: L 428 TYR cc_start: 0.6895 (p90) cc_final: 0.6344 (p90) REVERT: L 430 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.5134 (m-80) REVERT: M 365 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6707 (mpt-90) REVERT: N 455 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5436 (mp) REVERT: K 5 GLN cc_start: 0.8329 (mt0) cc_final: 0.7853 (mt0) outliers start: 112 outliers final: 45 residues processed: 572 average time/residue: 0.7430 time to fit residues: 515.2846 Evaluate side-chains 543 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 488 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 281 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 411 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 348 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 46 GLN G 765 GLN G 828 GLN C 16 GLN C 319 HIS ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077808 restraints weight = 40452.340| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.06 r_work: 0.3023 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38337 Z= 0.422 Angle : 2.506 50.804 52038 Z= 1.441 Chirality : 0.450 6.639 5793 Planarity : 0.005 0.050 6491 Dihedral : 9.420 115.243 5654 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 3.10 % Allowed : 14.57 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4675 helix: 1.32 (0.10), residues: 2693 sheet: -0.14 (0.30), residues: 320 loop : -0.36 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 85 TYR 0.024 0.002 TYR L 428 PHE 0.032 0.002 PHE N 72 TRP 0.020 0.002 TRP G 668 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01181 (38301) covalent geometry : angle 2.19259 (51945) hydrogen bonds : bond 0.06954 ( 1716) hydrogen bonds : angle 4.57701 ( 5148) metal coordination : bond 0.05527 ( 36) metal coordination : angle 28.79393 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 503 time to evaluate : 1.587 Fit side-chains REVERT: F 78 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7833 (mppt) REVERT: F 95 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: G 806 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: C 127 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8959 (t80) REVERT: C 400 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: B 39 MET cc_start: 0.7798 (tmm) cc_final: 0.7594 (tmm) REVERT: I 147 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: H 28 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8370 (m) REVERT: H 44 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: H 164 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7137 (mp) REVERT: H 238 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: H 281 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.5729 (mpp) REVERT: H 293 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7408 (ttp-110) REVERT: H 295 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7499 (OUTLIER) REVERT: L 428 TYR cc_start: 0.7090 (p90) cc_final: 0.6472 (p90) REVERT: L 430 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: M 365 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.6722 (mpt-90) REVERT: N 104 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: N 376 MET cc_start: 0.7134 (tpp) cc_final: 0.6865 (tpp) REVERT: K 5 GLN cc_start: 0.8377 (mt0) cc_final: 0.7905 (mt0) outliers start: 119 outliers final: 47 residues processed: 581 average time/residue: 0.7668 time to fit residues: 539.8525 Evaluate side-chains 544 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 483 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 281 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 91 optimal weight: 6.9990 chunk 380 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 397 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 252 optimal weight: 0.0270 chunk 11 optimal weight: 9.9990 chunk 330 optimal weight: 0.6980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN G 299 GLN C 16 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.100764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081674 restraints weight = 41154.382| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.06 r_work: 0.3105 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38337 Z= 0.386 Angle : 2.497 53.382 52038 Z= 1.435 Chirality : 0.442 6.452 5793 Planarity : 0.004 0.049 6491 Dihedral : 8.915 114.171 5654 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 2.73 % Allowed : 15.35 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4675 helix: 1.62 (0.10), residues: 2689 sheet: -0.08 (0.29), residues: 331 loop : -0.31 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 562 TYR 0.022 0.001 TYR M 435 PHE 0.032 0.001 PHE N 72 TRP 0.019 0.001 TRP H 260 HIS 0.011 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01125 (38301) covalent geometry : angle 2.17487 (51945) hydrogen bonds : bond 0.05219 ( 1716) hydrogen bonds : angle 4.26082 ( 5148) metal coordination : bond 0.03203 ( 36) metal coordination : angle 29.09960 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 516 time to evaluate : 1.506 Fit side-chains REVERT: F 78 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7827 (mppt) REVERT: F 95 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: G 252 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: G 804 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7780 (ttm-80) REVERT: C 30 ARG cc_start: 0.8247 (mpt-90) cc_final: 0.7981 (mpt-90) REVERT: C 127 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8831 (t80) REVERT: B 39 MET cc_start: 0.7782 (tmm) cc_final: 0.7523 (tmm) REVERT: I 84 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8382 (p0) REVERT: I 147 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: H 28 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8048 (m) REVERT: H 32 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5252 (mpt) REVERT: H 164 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6921 (mp) REVERT: H 238 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: H 293 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7339 (ttp-110) REVERT: H 295 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7529 (OUTLIER) REVERT: L 428 TYR cc_start: 0.6975 (p90) cc_final: 0.6272 (p90) REVERT: L 430 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.4948 (m-80) outliers start: 105 outliers final: 37 residues processed: 581 average time/residue: 0.7383 time to fit residues: 520.8863 Evaluate side-chains 547 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 499 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 312 optimal weight: 20.0000 chunk 419 optimal weight: 1.9990 chunk 335 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 175 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 435 HIS K 88 GLN J 86 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077741 restraints weight = 40223.868| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.05 r_work: 0.3022 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38337 Z= 0.429 Angle : 2.508 50.579 52038 Z= 1.441 Chirality : 0.451 6.634 5793 Planarity : 0.004 0.051 6491 Dihedral : 9.307 114.409 5650 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 2.81 % Allowed : 15.40 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4675 helix: 1.41 (0.10), residues: 2690 sheet: -0.10 (0.30), residues: 322 loop : -0.32 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 374 TYR 0.024 0.002 TYR N 260 PHE 0.031 0.002 PHE N 72 TRP 0.019 0.002 TRP H 260 HIS 0.010 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01196 (38301) covalent geometry : angle 2.19426 (51945) hydrogen bonds : bond 0.06913 ( 1716) hydrogen bonds : angle 4.56082 ( 5148) metal coordination : bond 0.05426 ( 36) metal coordination : angle 28.80252 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 497 time to evaluate : 1.917 Fit side-chains REVERT: F 78 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7822 (mppt) REVERT: F 95 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: G 806 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: C 127 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8979 (t80) REVERT: C 400 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: B 39 MET cc_start: 0.7834 (tmm) cc_final: 0.7454 (tmm) REVERT: I 147 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: H 44 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: H 164 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7184 (mp) REVERT: H 238 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: H 293 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7431 (ttp-110) REVERT: H 295 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7608 (OUTLIER) REVERT: A 102 GLU cc_start: 0.5784 (mt-10) cc_final: 0.5577 (mt-10) REVERT: L 428 TYR cc_start: 0.7128 (p90) cc_final: 0.6356 (p90) REVERT: L 430 PHE cc_start: 0.5927 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: K 5 GLN cc_start: 0.8397 (mt0) cc_final: 0.7916 (mt0) outliers start: 108 outliers final: 53 residues processed: 567 average time/residue: 0.7677 time to fit residues: 528.4348 Evaluate side-chains 548 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 485 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 314 ILE Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 137 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 311 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 438 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 149 optimal weight: 0.2980 chunk 463 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 238 ASN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN N 435 HIS K 88 GLN J 86 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080624 restraints weight = 40703.646| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.05 r_work: 0.3084 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 38337 Z= 0.389 Angle : 2.500 52.272 52038 Z= 1.436 Chirality : 0.444 6.535 5793 Planarity : 0.004 0.054 6491 Dihedral : 8.977 112.244 5649 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 2.34 % Allowed : 16.02 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4675 helix: 1.61 (0.10), residues: 2690 sheet: -0.08 (0.29), residues: 332 loop : -0.30 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 562 TYR 0.023 0.001 TYR L 428 PHE 0.031 0.001 PHE N 72 TRP 0.027 0.001 TRP H 260 HIS 0.010 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01131 (38301) covalent geometry : angle 2.17993 (51945) hydrogen bonds : bond 0.05544 ( 1716) hydrogen bonds : angle 4.32911 ( 5148) metal coordination : bond 0.03737 ( 36) metal coordination : angle 29.05361 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 497 time to evaluate : 1.603 Fit side-chains REVERT: F 78 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7807 (mppt) REVERT: F 95 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: G 804 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7616 (ttm110) REVERT: G 806 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: G 834 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: C 30 ARG cc_start: 0.8288 (mpt-90) cc_final: 0.7973 (mpt-90) REVERT: C 127 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8795 (t80) REVERT: B 39 MET cc_start: 0.7830 (tmm) cc_final: 0.7537 (tmm) REVERT: I 147 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: H 164 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7005 (mp) REVERT: H 238 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: H 293 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7362 (ttp-110) REVERT: H 295 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7607 (OUTLIER) REVERT: L 428 TYR cc_start: 0.7049 (p90) cc_final: 0.6383 (p90) REVERT: L 430 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5001 (m-80) REVERT: N 8 LEU cc_start: 0.7145 (tm) cc_final: 0.6622 (mt) REVERT: N 376 MET cc_start: 0.7265 (tpp) cc_final: 0.6842 (tpp) REVERT: K 5 GLN cc_start: 0.8343 (mt0) cc_final: 0.7862 (mt0) REVERT: K 26 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8112 (mtm180) outliers start: 90 outliers final: 46 residues processed: 558 average time/residue: 0.7514 time to fit residues: 511.0546 Evaluate side-chains 541 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 486 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 314 ILE Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 298 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 465 optimal weight: 10.0000 chunk 425 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 455 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS K 88 GLN J 86 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080616 restraints weight = 40491.288| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.05 r_work: 0.3085 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38337 Z= 0.390 Angle : 2.500 51.480 52038 Z= 1.436 Chirality : 0.444 6.522 5793 Planarity : 0.004 0.051 6491 Dihedral : 8.841 111.122 5644 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 2.24 % Allowed : 16.23 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.12), residues: 4675 helix: 1.64 (0.10), residues: 2688 sheet: -0.02 (0.29), residues: 331 loop : -0.28 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 859 TYR 0.023 0.001 TYR L 428 PHE 0.030 0.001 PHE N 72 TRP 0.031 0.001 TRP H 260 HIS 0.011 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01133 (38301) covalent geometry : angle 2.18070 (51945) hydrogen bonds : bond 0.05550 ( 1716) hydrogen bonds : angle 4.31168 ( 5148) metal coordination : bond 0.03930 ( 36) metal coordination : angle 29.00709 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 501 time to evaluate : 1.671 Fit side-chains REVERT: F 78 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7800 (mppt) REVERT: F 95 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: G 834 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: C 127 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8801 (t80) REVERT: B 39 MET cc_start: 0.7841 (tmm) cc_final: 0.7546 (tmm) REVERT: I 147 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: H 164 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6951 (mp) REVERT: H 238 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: H 293 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7362 (ttp-110) REVERT: H 295 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7640 (OUTLIER) REVERT: L 428 TYR cc_start: 0.7057 (p90) cc_final: 0.6389 (p90) REVERT: L 430 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: N 8 LEU cc_start: 0.7181 (tm) cc_final: 0.6638 (mt) REVERT: N 376 MET cc_start: 0.7233 (tpp) cc_final: 0.6899 (tpp) REVERT: K 5 GLN cc_start: 0.8347 (mt0) cc_final: 0.7865 (mt0) outliers start: 86 outliers final: 44 residues processed: 562 average time/residue: 0.7362 time to fit residues: 504.8163 Evaluate side-chains 542 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 490 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 176 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 chunk 255 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 464 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS K 88 GLN J 86 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079123 restraints weight = 40435.759| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.05 r_work: 0.3053 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38337 Z= 0.404 Angle : 2.506 50.649 52038 Z= 1.439 Chirality : 0.448 6.585 5793 Planarity : 0.004 0.061 6491 Dihedral : 8.972 109.855 5642 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 1.93 % Allowed : 16.68 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4675 helix: 1.57 (0.10), residues: 2688 sheet: -0.02 (0.30), residues: 322 loop : -0.30 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG L 562 TYR 0.026 0.002 TYR N 260 PHE 0.031 0.002 PHE N 72 TRP 0.034 0.001 TRP H 260 HIS 0.011 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01153 (38301) covalent geometry : angle 2.19017 (51945) hydrogen bonds : bond 0.06184 ( 1716) hydrogen bonds : angle 4.43118 ( 5148) metal coordination : bond 0.04773 ( 36) metal coordination : angle 28.90157 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 492 time to evaluate : 1.523 Fit side-chains REVERT: F 78 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7805 (mppt) REVERT: F 95 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: G 834 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: C 127 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8871 (t80) REVERT: B 39 MET cc_start: 0.7848 (tmm) cc_final: 0.7545 (tmm) REVERT: I 147 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: H 164 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7047 (mp) REVERT: H 238 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: H 293 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7404 (ttp-110) REVERT: L 428 TYR cc_start: 0.7109 (p90) cc_final: 0.6439 (p90) REVERT: L 430 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: N 8 LEU cc_start: 0.7312 (tm) cc_final: 0.6737 (mt) REVERT: N 376 MET cc_start: 0.7246 (tpp) cc_final: 0.6995 (tpp) REVERT: K 5 GLN cc_start: 0.8382 (mt0) cc_final: 0.7896 (mt0) outliers start: 74 outliers final: 45 residues processed: 540 average time/residue: 0.7763 time to fit residues: 509.0336 Evaluate side-chains 541 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 488 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 30 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 385 optimal weight: 6.9990 chunk 450 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 449 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS K 88 GLN J 86 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080185 restraints weight = 40224.651| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.05 r_work: 0.3075 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38337 Z= 0.394 Angle : 2.504 51.076 52038 Z= 1.438 Chirality : 0.445 6.517 5793 Planarity : 0.004 0.051 6491 Dihedral : 8.926 107.042 5642 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 1.74 % Allowed : 16.88 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 4675 helix: 1.62 (0.10), residues: 2692 sheet: -0.02 (0.29), residues: 333 loop : -0.29 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 374 TYR 0.023 0.002 TYR L 428 PHE 0.031 0.001 PHE N 72 TRP 0.038 0.001 TRP H 260 HIS 0.011 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01137 (38301) covalent geometry : angle 2.18589 (51945) hydrogen bonds : bond 0.05742 ( 1716) hydrogen bonds : angle 4.36570 ( 5148) metal coordination : bond 0.04052 ( 36) metal coordination : angle 28.99159 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 493 time to evaluate : 1.538 Fit side-chains REVERT: F 78 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7794 (mppt) REVERT: F 95 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: G 834 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: C 127 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8832 (t80) REVERT: C 216 MET cc_start: 0.7526 (ptm) cc_final: 0.6759 (ptp) REVERT: B 39 MET cc_start: 0.7848 (tmm) cc_final: 0.7546 (tmm) REVERT: I 147 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: H 164 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7022 (mp) REVERT: H 238 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: H 293 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7366 (ttp-110) REVERT: H 295 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7493 (OUTLIER) REVERT: L 428 TYR cc_start: 0.7072 (p90) cc_final: 0.6400 (p90) REVERT: L 430 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5011 (m-80) REVERT: N 8 LEU cc_start: 0.7340 (tm) cc_final: 0.6739 (mt) REVERT: N 376 MET cc_start: 0.7232 (tpp) cc_final: 0.6747 (tpp) REVERT: K 5 GLN cc_start: 0.8361 (mt0) cc_final: 0.7877 (mt0) outliers start: 67 outliers final: 45 residues processed: 538 average time/residue: 0.7728 time to fit residues: 504.8542 Evaluate side-chains 537 residues out of total 3855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 484 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 260 TRP Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 293 ARG Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 286 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 397 optimal weight: 9.9990 chunk 433 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 445 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN G 54 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS N 149 GLN N 435 HIS J 86 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077155 restraints weight = 39724.392| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.04 r_work: 0.3011 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38337 Z= 0.441 Angle : 2.521 50.619 52038 Z= 1.447 Chirality : 0.452 6.676 5793 Planarity : 0.005 0.059 6491 Dihedral : 9.420 105.433 5642 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.85 % Allowed : 16.81 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 4675 helix: 1.34 (0.10), residues: 2697 sheet: -0.11 (0.30), residues: 323 loop : -0.33 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 562 TYR 0.026 0.002 TYR N 260 PHE 0.031 0.002 PHE N 72 TRP 0.033 0.002 TRP H 260 HIS 0.011 0.002 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01217 (38301) covalent geometry : angle 2.20992 (51945) hydrogen bonds : bond 0.07270 ( 1716) hydrogen bonds : angle 4.66623 ( 5148) metal coordination : bond 0.05869 ( 36) metal coordination : angle 28.79856 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22257.34 seconds wall clock time: 377 minutes 16.64 seconds (22636.64 seconds total)