Starting phenix.real_space_refine on Fri Jan 16 15:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7s_14536/01_2026/7z7s_14536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7s_14536/01_2026/7z7s_14536.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/7z7s_14536/01_2026/7z7s_14536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7s_14536/01_2026/7z7s_14536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7s_14536/01_2026/7z7s_14536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7s_14536/01_2026/7z7s_14536.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= 0.024 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 16 5.49 5 S 268 5.16 5 C 24746 2.51 5 N 6274 2.21 5 O 7871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s 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: 39208 Number of models: 1 Model: "" Number of chains: 37 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: 7017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7017 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 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: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "L" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4558 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 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: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3601 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 454} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'DCQ': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 217 Unusual residues: {'3PE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "M" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "G" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 353 Classifications: {'water': 353} Link IDs: {None: 352} Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "I" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 73.008 61.008 190.032 1.00 10.28 S ATOM 2741 SG CYS F 357 76.234 60.572 194.427 1.00 13.76 S ATOM 3062 SG CYS F 398 70.497 57.112 194.878 1.00 20.39 S ATOM 2697 SG CYS F 351 75.073 54.627 191.425 1.00 9.57 S ATOM 4054 SG CYS E 92 83.146 53.375 211.387 1.00 22.13 S ATOM 4088 SG CYS E 97 83.181 54.011 214.921 1.00 21.77 S ATOM 4366 SG CYS E 133 77.962 52.650 210.916 1.00 33.26 S ATOM 4392 SG CYS E 137 77.081 53.384 214.127 1.00 34.35 S ATOM 5472 SG CYS G 114 83.693 66.810 172.593 1.00 18.98 S ATOM 5412 SG CYS G 105 88.820 70.833 174.077 1.00 26.30 S ATOM 5432 SG CYS G 108 89.624 64.686 172.104 1.00 15.17 S ATOM 5826 SG CYS G 156 77.956 59.074 177.587 1.00 31.65 S ATOM 5807 SG CYS G 153 83.748 58.027 180.776 1.00 11.11 S ATOM 5855 SG CYS G 159 81.032 53.418 177.225 1.00 8.58 S ATOM 6203 SG CYS G 203 83.085 58.553 174.047 1.00 14.69 S ATOM 6428 SG CYS G 230 80.336 49.681 153.065 1.00 18.19 S ATOM 6713 SG CYS G 265 80.174 45.972 158.417 1.00 13.70 S ATOM 6476 SG CYS G 237 74.900 49.336 156.068 1.00 17.42 S ATOM 6452 SG CYS G 233 77.259 43.965 153.091 1.00 15.96 S ATOM 4877 SG CYS G 36 71.454 60.004 180.214 1.00 9.07 S ATOM 4953 SG CYS G 47 72.999 63.443 180.586 1.00 10.32 S ATOM 4979 SG CYS G 50 67.273 65.016 180.242 1.00 16.11 S ATOM 5124 SG CYS G 69 66.746 61.423 179.981 1.00 17.16 S ATOM 17375 SG CYS B 129 93.858 93.730 148.704 1.00 12.15 S ATOM 16872 SG CYS B 64 99.051 97.647 150.215 1.00 8.28 S ATOM 16866 SG CYS B 63 93.442 99.648 152.066 1.00 13.36 S ATOM 17592 SG CYS B 158 95.672 93.802 154.332 1.00 13.04 S ATOM 18923 SG CYS I 102 94.403 88.050 160.484 1.00 13.27 S ATOM 18898 SG CYS I 99 99.999 86.767 156.959 1.00 14.68 S ATOM 18941 SG CYS I 105 98.433 83.577 162.420 1.00 22.40 S ATOM 18656 SG CYS I 70 94.637 82.775 157.192 1.00 29.28 S ATOM 18970 SG CYS I 109 99.385 78.229 168.776 1.00 10.56 S ATOM 18633 SG CYS I 66 97.559 77.383 162.613 1.00 12.18 S ATOM 18593 SG CYS I 60 101.716 73.180 164.984 1.00 11.51 S ATOM 18611 SG CYS I 63 95.403 73.685 167.373 1.00 13.63 S Time building chain proxies: 8.83, per 1000 atoms: 0.23 Number of scatterers: 39208 At special positions: 0 Unit cell: (157, 217.5, 241, 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 268 16.00 P 16 15.00 O 7871 8.00 N 6274 7.00 C 24746 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: 3.63 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " 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="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " 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 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8724 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 51.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 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: 4.744A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.534A 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: 4.613A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 5.079A 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: 5.015A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE G 770 " --> pdb=" O ALA G 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 770' 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: 5.077A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.451A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 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 removed outlier: 4.015A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) 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: 4.876A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 removed outlier: 4.171A pdb=" N PHE I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) 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: 5.178A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.763A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.450A pdb=" N VAL H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.964A 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 68 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.360A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) 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: 4.219A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.856A 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: 4.498A 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: 5.138A 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: 4.679A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.395A 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 removed outlier: 4.338A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) 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: 4.595A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.437A 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: 4.266A 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: 4.319A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.549A 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: 4.237A 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 80 through 84 Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.173A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1702 hydrogen bonds defined for protein. 5106 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: 6.60 Time building geometry restraints manager: 4.79 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: 16139 1.42 - 1.64: 22323 1.64 - 1.86: 411 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38965 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.43e+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 1.31e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.605 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.378 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O5D NAI F 503 " pdb=" PN NAI F 503 " ideal model delta sigma weight residual 1.650 1.586 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 38960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 52241 3.07 - 6.14: 473 6.14 - 9.21: 98 9.21 - 12.28: 9 12.28 - 15.36: 4 Bond angle restraints: 52825 Sorted by residual: angle pdb=" CA VAL K 95 " pdb=" CB VAL K 95 " pdb=" CG1 VAL K 95 " ideal model delta sigma weight residual 110.40 119.60 -9.20 1.70e+00 3.46e-01 2.93e+01 angle pdb=" CB MET H 232 " pdb=" CG MET H 232 " pdb=" SD MET H 232 " ideal model delta sigma weight residual 112.70 128.06 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CB LYS L 162 " pdb=" CG LYS L 162 " pdb=" CD LYS L 162 " ideal model delta sigma weight residual 111.30 122.55 -11.25 2.30e+00 1.89e-01 2.39e+01 angle pdb=" C ILE N 3 " pdb=" N THR N 4 " pdb=" CA THR N 4 " ideal model delta sigma weight residual 120.68 127.83 -7.15 1.52e+00 4.33e-01 2.21e+01 angle pdb=" S3 SF4 F 501 " pdb="FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.96 -6.86 1.50e+00 4.44e-01 2.09e+01 ... (remaining 52820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 21256 24.32 - 48.63: 1477 48.63 - 72.95: 263 72.95 - 97.27: 47 97.27 - 121.59: 6 Dihedral angle restraints: 23049 sinusoidal: 9409 harmonic: 13640 Sorted by residual: dihedral pdb=" CA ALA G 177 " pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA LYS C 69 " pdb=" C LYS C 69 " pdb=" N PRO C 70 " pdb=" CA PRO C 70 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 23046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 5839 4.245 - 8.490: 0 8.490 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.226: 28 Chirality restraints: 5867 Sorted by residual: 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 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.66 -21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.65 21.21 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5864 not shown) Planarity restraints: 6595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 702 " -0.029 2.00e-02 2.50e+03 5.53e-02 9.17e+01 pdb=" C1M DCQ C 702 " -0.086 2.00e-02 2.50e+03 pdb=" C2 DCQ C 702 " -0.007 2.00e-02 2.50e+03 pdb=" C3 DCQ C 702 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DCQ C 702 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DCQ C 702 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DCQ C 702 " 0.038 2.00e-02 2.50e+03 pdb=" C7 DCQ C 702 " 0.097 2.00e-02 2.50e+03 pdb=" O2 DCQ C 702 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ C 702 " 0.100 2.00e-02 2.50e+03 pdb=" O4 DCQ C 702 " -0.081 2.00e-02 2.50e+03 pdb=" O5 DCQ C 702 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.018 2.00e-02 2.50e+03 2.67e-02 2.13e+01 pdb=" C1M DCQ B 302 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " 0.001 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.058 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " 0.015 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " 0.033 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.016 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO G 764 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.036 5.00e-02 4.00e+02 ... (remaining 6592 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6287 2.76 - 3.29: 38382 3.29 - 3.83: 77550 3.83 - 4.36: 94968 4.36 - 4.90: 151674 Nonbonded interactions: 368861 Sorted by model distance: nonbonded pdb=" OD1 ASN C 223 " pdb=" OH TYR B 57 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU I 169 " pdb=" O HOH I 301 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP C 342 " pdb=" OH TYR C 394 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.238 3.040 nonbonded pdb=" O TYR E 76 " pdb=" O HOH E 301 " model vdw 2.244 3.040 ... (remaining 368856 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: 5.940 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: 3.230 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 40.670 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 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 : 0.007 0.147 39001 Z= 0.296 Angle : 0.838 15.356 52918 Z= 0.420 Chirality : 1.462 21.226 5867 Planarity : 0.006 0.073 6595 Dihedral : 16.749 121.586 14325 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % Rotamer: Outliers : 1.67 % Allowed : 16.39 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.03 (0.11), residues: 4740 helix: 0.47 (0.09), residues: 2694 sheet: -0.39 (0.28), residues: 319 loop : -0.56 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 374 TYR 0.030 0.003 TYR H 156 PHE 0.037 0.002 PHE L 341 TRP 0.022 0.002 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00676 (38965) covalent geometry : angle 0.81602 (52825) hydrogen bonds : bond 0.07484 ( 1702) hydrogen bonds : angle 4.84169 ( 5106) metal coordination : bond 0.05369 ( 36) metal coordination : angle 4.59942 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 536 time to evaluate : 1.666 Fit side-chains REVERT: F 243 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8630 (mttp) REVERT: G 906 LYS cc_start: 0.8904 (pttm) cc_final: 0.8635 (pmtt) REVERT: C 202 GLU cc_start: 0.8826 (mp0) cc_final: 0.8530 (pm20) REVERT: C 333 MET cc_start: 0.8110 (ptt) cc_final: 0.7431 (ppp) REVERT: B 219 GLU cc_start: 0.8396 (pm20) cc_final: 0.7848 (mm-30) REVERT: H 80 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7283 (ttt-90) REVERT: L 515 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8559 (tptp) REVERT: M 145 MET cc_start: 0.8341 (ttm) cc_final: 0.7949 (ppp) REVERT: N 200 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7840 (tm-30) outliers start: 65 outliers final: 40 residues processed: 589 average time/residue: 0.8138 time to fit residues: 572.6010 Evaluate side-chains 561 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 520 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 314 SER Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 332 THR Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 386 GLN E 82 GLN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 845 ASN C 31 ASN C 190 GLN C 319 HIS H 323 GLN M 179 GLN N 285 ASN N 447 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070767 restraints weight = 34267.783| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 0.89 r_work: 0.2834 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.279 39001 Z= 0.387 Angle : 2.472 56.622 52918 Z= 1.421 Chirality : 0.440 6.598 5867 Planarity : 0.004 0.056 6595 Dihedral : 9.788 116.875 5919 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.04 % Rotamer: Outliers : 2.26 % Allowed : 15.59 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 4740 helix: 1.22 (0.10), residues: 2698 sheet: -0.17 (0.28), residues: 314 loop : -0.44 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.024 0.001 TYR L 428 PHE 0.028 0.001 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01130 (38965) covalent geometry : angle 2.15254 (52825) hydrogen bonds : bond 0.05122 ( 1702) hydrogen bonds : angle 4.26685 ( 5106) metal coordination : bond 0.04110 ( 36) metal coordination : angle 29.09242 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 547 time to evaluate : 1.724 Fit side-chains REVERT: F 32 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8854 (ptmt) REVERT: G 187 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: G 906 LYS cc_start: 0.8725 (pttm) cc_final: 0.8441 (pmtt) REVERT: C 165 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8819 (mmmt) REVERT: C 202 GLU cc_start: 0.8281 (mp0) cc_final: 0.8036 (mp0) REVERT: C 333 MET cc_start: 0.7851 (ptt) cc_final: 0.7227 (ppp) REVERT: I 86 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8951 (ttt90) REVERT: L 175 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8596 (tpt-90) REVERT: L 529 ARG cc_start: 0.8465 (tpp80) cc_final: 0.8014 (ttm170) REVERT: M 145 MET cc_start: 0.8008 (ttm) cc_final: 0.7792 (ppp) REVERT: M 209 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8182 (mp0) outliers start: 88 outliers final: 40 residues processed: 603 average time/residue: 0.8340 time to fit residues: 601.9777 Evaluate side-chains 562 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 517 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU 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 301 ASP Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 465 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 386 GLN G 828 GLN G 845 ASN G 901 HIS C 31 ASN H 261 GLN M 179 GLN N 447 ASN K 5 GLN K 88 GLN J 75 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.067987 restraints weight = 33800.717| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 0.89 r_work: 0.2769 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 39001 Z= 0.401 Angle : 2.471 50.842 52918 Z= 1.422 Chirality : 0.446 6.587 5867 Planarity : 0.004 0.053 6595 Dihedral : 9.585 113.303 5883 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 2.87 % Allowed : 15.11 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4740 helix: 1.44 (0.10), residues: 2705 sheet: 0.01 (0.29), residues: 311 loop : -0.34 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 30 TYR 0.021 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01145 (38965) covalent geometry : angle 2.15825 (52825) hydrogen bonds : bond 0.05922 ( 1702) hydrogen bonds : angle 4.29188 ( 5106) metal coordination : bond 0.05277 ( 36) metal coordination : angle 28.76712 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 538 time to evaluate : 1.235 Fit side-chains REVERT: F 32 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8714 (ptmt) REVERT: F 158 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8593 (mttm) REVERT: G 64 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8387 (ptt-90) REVERT: G 187 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: G 906 LYS cc_start: 0.8754 (pttm) cc_final: 0.8466 (pmtt) REVERT: C 165 LYS cc_start: 0.9065 (mmpt) cc_final: 0.8816 (mmmt) REVERT: C 333 MET cc_start: 0.8126 (ptt) cc_final: 0.7598 (ppp) REVERT: I 86 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8969 (ttt90) REVERT: I 171 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8741 (mtpt) REVERT: H 80 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7047 (ttt-90) REVERT: L 577 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7736 (mtt90) REVERT: L 581 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8308 (mtpt) REVERT: M 145 MET cc_start: 0.8126 (ttm) cc_final: 0.7889 (ppp) REVERT: M 209 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: J 75 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7347 (p0) outliers start: 112 outliers final: 53 residues processed: 604 average time/residue: 0.8027 time to fit residues: 580.3555 Evaluate side-chains 581 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 520 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 311 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 346 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 258 ASN F 386 GLN G 655 HIS G 845 ASN G 901 HIS C 31 ASN H 261 GLN M 179 GLN M 403 ASN N 285 ASN N 305 HIS K 5 GLN J 75 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066857 restraints weight = 33368.264| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 0.89 r_work: 0.2742 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 39001 Z= 0.415 Angle : 2.474 50.569 52918 Z= 1.424 Chirality : 0.449 6.647 5867 Planarity : 0.004 0.053 6595 Dihedral : 9.757 110.867 5878 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 2.87 % Allowed : 15.00 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4740 helix: 1.44 (0.10), residues: 2706 sheet: 0.02 (0.29), residues: 311 loop : -0.27 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 374 TYR 0.020 0.002 TYR L 428 PHE 0.026 0.002 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.012 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01169 (38965) covalent geometry : angle 2.16378 (52825) hydrogen bonds : bond 0.06429 ( 1702) hydrogen bonds : angle 4.37755 ( 5106) metal coordination : bond 0.05198 ( 36) metal coordination : angle 28.70393 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 531 time to evaluate : 1.534 Fit side-chains REVERT: F 32 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8849 (ptmt) REVERT: F 158 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8645 (mttm) REVERT: E 103 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: G 64 ARG cc_start: 0.8615 (ttp-170) cc_final: 0.8380 (ptt-90) REVERT: G 187 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: G 789 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: G 906 LYS cc_start: 0.8755 (pttm) cc_final: 0.8453 (pmtt) REVERT: C 490 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 197 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: I 93 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.7544 (ttp80) REVERT: H 32 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7635 (tmm) REVERT: H 80 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7100 (ttt-90) REVERT: L 506 LEU cc_start: 0.8622 (mt) cc_final: 0.8421 (mp) REVERT: L 529 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8040 (ttm170) REVERT: L 577 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7869 (mtt90) REVERT: L 581 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8344 (mtpt) REVERT: M 145 MET cc_start: 0.8209 (ttm) cc_final: 0.7975 (ppp) REVERT: M 209 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: J 102 ILE cc_start: 0.8425 (pt) cc_final: 0.8176 (mt) outliers start: 112 outliers final: 59 residues processed: 599 average time/residue: 0.8446 time to fit residues: 602.7184 Evaluate side-chains 588 residues out of total 3905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 519 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 723 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 93 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8085 > 50: distance: 51 - 53: 24.597 distance: 53 - 54: 38.829 distance: 54 - 55: 18.803 distance: 54 - 57: 16.271 distance: 55 - 56: 23.875 distance: 55 - 61: 34.604 distance: 57 - 58: 22.616 distance: 57 - 59: 21.976 distance: 58 - 60: 27.027 distance: 61 - 62: 13.530 distance: 62 - 63: 7.024 distance: 62 - 65: 24.003 distance: 63 - 64: 23.931 distance: 65 - 66: 26.610 distance: 66 - 67: 31.794 distance: 67 - 68: 28.928 distance: 68 - 69: 10.062 distance: 70 - 71: 17.690 distance: 71 - 72: 19.819 distance: 71 - 74: 28.532 distance: 72 - 73: 15.914 distance: 72 - 79: 11.116 distance: 74 - 75: 33.723 distance: 75 - 76: 14.181 distance: 76 - 77: 14.106 distance: 76 - 78: 15.113 distance: 79 - 80: 19.780 distance: 79 - 85: 21.607 distance: 80 - 81: 23.239 distance: 80 - 83: 15.934 distance: 81 - 82: 11.348 distance: 81 - 86: 22.614 distance: 83 - 84: 28.112 distance: 84 - 85: 33.802 distance: 86 - 87: 10.597 distance: 87 - 88: 8.940 distance: 87 - 90: 11.802 distance: 88 - 89: 18.219 distance: 88 - 97: 11.545 distance: 90 - 91: 8.047 distance: 91 - 92: 15.954 distance: 91 - 93: 26.055 distance: 92 - 94: 19.727 distance: 93 - 95: 24.967 distance: 94 - 96: 24.251 distance: 95 - 96: 20.192 distance: 97 - 98: 23.512 distance: 98 - 99: 17.476 distance: 98 - 101: 38.454 distance: 99 - 100: 18.642 distance: 99 - 103: 14.314 distance: 103 - 104: 19.318 distance: 104 - 105: 13.895 distance: 104 - 107: 14.182 distance: 105 - 106: 8.468 distance: 105 - 111: 14.727 distance: 107 - 108: 13.106 distance: 108 - 109: 7.333 distance: 108 - 110: 10.115 distance: 111 - 112: 4.131 distance: 112 - 113: 11.184 distance: 112 - 115: 11.311 distance: 113 - 114: 12.904 distance: 113 - 118: 19.075 distance: 115 - 116: 11.324 distance: 115 - 117: 3.740 distance: 118 - 119: 14.463 distance: 119 - 120: 7.761 distance: 119 - 122: 11.952 distance: 120 - 121: 4.269 distance: 120 - 128: 13.416 distance: 122 - 123: 8.724 distance: 123 - 124: 19.980 distance: 123 - 125: 24.640 distance: 124 - 126: 8.131 distance: 125 - 127: 21.364 distance: 126 - 127: 28.658 distance: 128 - 129: 5.113 distance: 129 - 130: 10.031 distance: 129 - 132: 12.873 distance: 130 - 131: 14.123 distance: 130 - 136: 7.784 distance: 132 - 133: 5.406 distance: 133 - 134: 12.335 distance: 133 - 135: 8.897