Starting phenix.real_space_refine on Fri Jan 16 15:13:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7v_14538/01_2026/7z7v_14538.cif" } resolution = 2.29 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= 0.025 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 15 5.49 5 S 267 5.16 5 C 24630 2.51 5 N 6229 2.21 5 O 7932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 39106 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: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4739 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 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: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2544 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 307} Chain: "A" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 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: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 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: "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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'3PE': 1, 'C14': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 374 Classifications: {'water': 374} Link IDs: {None: 373} Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} 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: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "M" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.753 59.429 190.607 1.00 10.59 S ATOM 2741 SG CYS F 357 75.166 58.851 194.926 1.00 14.52 S ATOM 3062 SG CYS F 398 69.352 55.472 195.437 1.00 13.88 S ATOM 2697 SG CYS F 351 73.808 53.023 191.808 1.00 10.92 S ATOM 4054 SG CYS E 92 82.241 51.041 211.539 1.00 25.54 S ATOM 4088 SG CYS E 97 82.422 51.635 215.035 1.00 25.17 S ATOM 4366 SG CYS E 133 77.020 50.435 211.204 1.00 24.06 S ATOM 4392 SG CYS E 137 76.216 51.120 214.410 1.00 27.51 S ATOM 5476 SG CYS G 114 82.160 65.592 173.117 1.00 6.97 S ATOM 5416 SG CYS G 105 87.394 69.435 174.625 1.00 8.64 S ATOM 5436 SG CYS G 108 88.084 63.362 172.468 1.00 7.80 S ATOM 5830 SG CYS G 156 76.438 57.807 178.031 1.00 10.63 S ATOM 5811 SG CYS G 153 82.288 56.614 181.072 1.00 5.16 S ATOM 5859 SG CYS G 159 79.434 52.126 177.434 1.00 7.28 S ATOM 6207 SG CYS G 203 81.495 57.308 174.373 1.00 25.66 S ATOM 6432 SG CYS G 230 78.189 49.027 153.199 1.00 17.55 S ATOM 6717 SG CYS G 265 78.089 45.164 158.494 1.00 11.97 S ATOM 6480 SG CYS G 237 72.808 48.663 156.330 1.00 16.45 S ATOM 6456 SG CYS G 233 75.039 43.341 153.193 1.00 20.81 S ATOM 4877 SG CYS G 36 69.939 58.750 180.890 1.00 9.54 S ATOM 4953 SG CYS G 47 71.584 62.139 181.258 1.00 9.54 S ATOM 4979 SG CYS G 50 65.842 63.831 181.095 1.00 12.55 S ATOM 5128 SG CYS G 69 65.248 60.283 180.730 1.00 13.56 S ATOM 17239 SG CYS B 129 92.330 92.840 149.583 1.00 17.15 S ATOM 16736 SG CYS B 64 97.575 96.626 151.122 1.00 12.09 S ATOM 16730 SG CYS B 63 92.000 98.680 153.046 1.00 12.79 S ATOM 17456 SG CYS B 158 94.176 92.762 155.231 1.00 11.08 S ATOM 18787 SG CYS I 102 92.985 86.937 161.295 1.00 11.95 S ATOM 18762 SG CYS I 99 98.492 85.662 157.637 1.00 11.64 S ATOM 18805 SG CYS I 105 96.998 82.327 163.033 1.00 14.73 S ATOM 18520 SG CYS I 70 93.101 81.722 157.838 1.00 12.01 S ATOM 18834 SG CYS I 109 97.990 76.801 169.253 1.00 7.72 S ATOM 18497 SG CYS I 66 96.041 76.117 163.128 1.00 10.18 S ATOM 18457 SG CYS I 60 100.143 71.783 165.326 1.00 8.11 S ATOM 18475 SG CYS I 63 93.870 72.375 167.862 1.00 11.14 S Time building chain proxies: 8.25, per 1000 atoms: 0.21 Number of scatterers: 39106 At special positions: 0 Unit cell: (157, 214.5, 241.5, 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 267 16.00 P 15 15.00 O 7932 8.00 N 6229 7.00 C 24630 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: 3.31 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 133 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " 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 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8674 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 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: 4.740A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.529A 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: 4.576A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 5.014A 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: 5.002A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.365A 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: 5.068A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.007A 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 removed outlier: 4.080A 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 removed outlier: 4.008A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) 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: 4.783A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.312A 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: 4.844A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.015A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.925A 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 removed outlier: 4.326A 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: 4.663A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 5.007A 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: 4.643A 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: 5.156A 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: 4.717A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.293A 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: 4.106A 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: 4.473A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.259A 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: 4.201A 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: 4.276A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.560A 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: 4.276A 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: 5.439A 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 1714 hydrogen bonds defined for protein. 5142 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: 6.80 Time building geometry restraints manager: 4.27 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: 16038 1.42 - 1.64: 22208 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38747 Sorted by residual: 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 2.44e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.604 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.382 0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.99e+00 ... (remaining 38742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 51890 2.84 - 5.67: 523 5.67 - 8.51: 90 8.51 - 11.35: 11 11.35 - 14.18: 4 Bond angle restraints: 52518 Sorted by residual: angle pdb=" CG1 ILE M 109 " pdb=" CB ILE M 109 " pdb=" CG2 ILE M 109 " ideal model delta sigma weight residual 110.70 96.52 14.18 3.00e+00 1.11e-01 2.24e+01 angle pdb=" S3 SF4 F 501 " pdb="FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.61 -6.51 1.50e+00 4.44e-01 1.88e+01 angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 121.57 -7.67 1.80e+00 3.09e-01 1.82e+01 angle pdb=" S3 SF4 F 501 " pdb="FE2 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.29 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CA LEU N 313 " pdb=" CB LEU N 313 " pdb=" CG LEU N 313 " ideal model delta sigma weight residual 116.30 130.24 -13.94 3.50e+00 8.16e-02 1.59e+01 ... (remaining 52513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 20933 23.40 - 46.81: 1613 46.81 - 70.21: 308 70.21 - 93.61: 62 93.61 - 117.02: 5 Dihedral angle restraints: 22921 sinusoidal: 9360 harmonic: 13561 Sorted by residual: 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 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA PRO N 387 " pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA THR L 257 " pdb=" C THR L 257 " pdb=" N MET L 258 " pdb=" CA MET L 258 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 22918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.249: 5810 4.249 - 8.499: 0 8.499 - 12.748: 0 12.748 - 16.998: 0 16.998 - 21.247: 28 Chirality restraints: 5838 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 10.69 -21.25 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 10.65 -21.20 2.00e-01 2.50e+01 1.12e+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 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5835 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO J 90 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO G 764 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 357 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C CYS F 357 " -0.044 2.00e-02 2.50e+03 pdb=" O CYS F 357 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG F 358 " 0.015 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8550 2.77 - 3.31: 37734 3.31 - 3.84: 77907 3.84 - 4.37: 93771 4.37 - 4.90: 149838 Nonbonded interactions: 367800 Sorted by model distance: nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN G 768 " pdb=" O HOH G1101 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.250 3.040 nonbonded pdb=" O ALA N 312 " pdb=" OG SER N 322 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP A 124 " pdb=" O HOH A 301 " model vdw 2.263 3.040 ... (remaining 367795 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.180 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 37.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 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 0.153 38783 Z= 0.251 Angle : 0.784 14.794 52611 Z= 0.393 Chirality : 1.465 21.247 5838 Planarity : 0.006 0.106 6552 Dihedral : 17.061 117.017 14247 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 1.68 % Allowed : 17.87 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 0.25 (0.11), residues: 4710 helix: 0.66 (0.09), residues: 2718 sheet: -0.13 (0.28), residues: 311 loop : -0.41 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 287 TYR 0.027 0.002 TYR H 242 PHE 0.037 0.002 PHE L 341 TRP 0.019 0.002 TRP M 122 HIS 0.010 0.001 HIS N 368 Details of bonding type rmsd covalent geometry : bond 0.00549 (38747) covalent geometry : angle 0.76177 (52518) hydrogen bonds : bond 0.07107 ( 1714) hydrogen bonds : angle 4.76334 ( 5142) metal coordination : bond 0.05593 ( 36) metal coordination : angle 4.50333 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 558 time to evaluate : 1.309 Fit side-chains REVERT: E 45 LYS cc_start: 0.9202 (tppt) cc_final: 0.8792 (tmmt) REVERT: E 103 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: E 163 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8142 (mm-30) REVERT: G 874 GLU cc_start: 0.8437 (pt0) cc_final: 0.7864 (pt0) REVERT: I 153 MET cc_start: 0.8856 (mmt) cc_final: 0.8628 (mmm) REVERT: L 379 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8620 (t80) REVERT: L 529 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8134 (ttp-170) REVERT: N 1 MET cc_start: 0.6654 (mtp) cc_final: 0.6413 (mtt) REVERT: J 72 MET cc_start: 0.8784 (mtt) cc_final: 0.8568 (mtt) outliers start: 65 outliers final: 41 residues processed: 609 average time/residue: 0.7912 time to fit residues: 574.5409 Evaluate side-chains 555 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 511 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 489 SER Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 529 ARG Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 8.9990 overall best weight: 2.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 728 GLN C 219 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN C 359 HIS H 138 ASN H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN M 344 GLN M 441 HIS N 285 ASN K 27 ASN K 82 GLN J 22 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.067725 restraints weight = 30283.798| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 0.90 r_work: 0.2752 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.260 38783 Z= 0.392 Angle : 2.481 51.079 52611 Z= 1.429 Chirality : 0.440 6.476 5838 Planarity : 0.004 0.068 6552 Dihedral : 9.671 111.436 5894 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 16.24 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.01 (0.12), residues: 4710 helix: 1.35 (0.10), residues: 2733 sheet: 0.02 (0.30), residues: 298 loop : -0.22 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 378 TYR 0.022 0.002 TYR L 428 PHE 0.028 0.001 PHE L 341 TRP 0.018 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01131 (38747) covalent geometry : angle 2.16468 (52518) hydrogen bonds : bond 0.05725 ( 1714) hydrogen bonds : angle 4.30464 ( 5142) metal coordination : bond 0.05218 ( 36) metal coordination : angle 28.90386 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 530 time to evaluate : 1.649 Fit side-chains REVERT: E 90 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8234 (mtt90) REVERT: M 462 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8473 (tm) REVERT: N 1 MET cc_start: 0.6983 (mtp) cc_final: 0.6757 (mtt) REVERT: N 427 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8283 (ttm110) REVERT: J 69 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8328 (t80) outliers start: 93 outliers final: 38 residues processed: 586 average time/residue: 0.8809 time to fit residues: 610.1858 Evaluate side-chains 567 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 526 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 427 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 221 optimal weight: 10.0000 chunk 451 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 383 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 261 optimal weight: 0.0870 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 172 HIS G 232 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN L 438 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 285 ASN K 27 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.064325 restraints weight = 30162.470| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 0.89 r_work: 0.2669 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38783 Z= 0.425 Angle : 2.484 50.491 52611 Z= 1.430 Chirality : 0.450 6.706 5838 Planarity : 0.005 0.056 6552 Dihedral : 9.731 104.444 5859 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 2.78 % Allowed : 15.06 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.25 (0.12), residues: 4710 helix: 1.51 (0.10), residues: 2732 sheet: 0.17 (0.30), residues: 297 loop : -0.07 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 91 TYR 0.020 0.002 TYR H 242 PHE 0.027 0.002 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.008 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01185 (38747) covalent geometry : angle 2.17278 (52518) hydrogen bonds : bond 0.07197 ( 1714) hydrogen bonds : angle 4.51784 ( 5142) metal coordination : bond 0.05902 ( 36) metal coordination : angle 28.69462 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 539 time to evaluate : 1.744 Fit side-chains REVERT: E 90 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8579 (mtm-85) REVERT: G 482 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: G 486 ASP cc_start: 0.8267 (m-30) cc_final: 0.7847 (m-30) REVERT: G 874 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: G 903 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 124 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: M 209 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: M 456 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: M 462 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8544 (tm) REVERT: N 1 MET cc_start: 0.6998 (mtp) cc_final: 0.6776 (mtt) REVERT: N 197 MET cc_start: 0.8220 (mmm) cc_final: 0.7992 (mmt) REVERT: J 59 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8992 (t80) REVERT: J 69 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8456 (t80) outliers start: 108 outliers final: 44 residues processed: 604 average time/residue: 0.8780 time to fit residues: 629.7222 Evaluate side-chains 581 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 528 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL 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 574 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 456 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 78 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN M 441 HIS K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066704 restraints weight = 30353.844| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 0.85 r_work: 0.2729 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38783 Z= 0.392 Angle : 2.474 50.643 52611 Z= 1.425 Chirality : 0.445 6.571 5838 Planarity : 0.004 0.051 6552 Dihedral : 9.356 105.865 5855 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Rotamer: Outliers : 2.27 % Allowed : 15.60 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.42 (0.12), residues: 4710 helix: 1.69 (0.10), residues: 2738 sheet: 0.18 (0.30), residues: 298 loop : -0.07 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 287 TYR 0.021 0.002 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.020 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01130 (38747) covalent geometry : angle 2.15895 (52518) hydrogen bonds : bond 0.05954 ( 1714) hydrogen bonds : angle 4.31336 ( 5142) metal coordination : bond 0.04232 ( 36) metal coordination : angle 28.82335 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 538 time to evaluate : 1.650 Fit side-chains REVERT: E 90 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8532 (mtm-85) REVERT: G 428 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8538 (ptpp) REVERT: G 903 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: I 153 MET cc_start: 0.8750 (mmt) cc_final: 0.8486 (mmm) REVERT: H 36 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 81 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 124 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: L 51 ASP cc_start: 0.8479 (t70) cc_final: 0.8070 (t0) REVERT: L 110 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: M 456 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: M 462 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8538 (tm) REVERT: N 1 MET cc_start: 0.6980 (mtp) cc_final: 0.6715 (mtt) REVERT: N 197 MET cc_start: 0.8192 (mmm) cc_final: 0.7970 (mmt) REVERT: J 69 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8446 (t80) outliers start: 88 outliers final: 41 residues processed: 594 average time/residue: 0.8749 time to fit residues: 617.5503 Evaluate side-chains 562 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 512 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 294 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 451 optimal weight: 0.8980 chunk 373 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 461 optimal weight: 0.0270 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 163 ASN L 212 ASN M 441 HIS N 285 ASN K 27 ASN K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067162 restraints weight = 30673.801| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 0.90 r_work: 0.2737 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38783 Z= 0.387 Angle : 2.473 50.593 52611 Z= 1.424 Chirality : 0.444 6.525 5838 Planarity : 0.004 0.049 6552 Dihedral : 9.082 105.983 5854 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 15.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.52 (0.12), residues: 4710 helix: 1.78 (0.10), residues: 2742 sheet: 0.25 (0.31), residues: 298 loop : -0.05 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 287 TYR 0.022 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01123 (38747) covalent geometry : angle 2.15601 (52518) hydrogen bonds : bond 0.05618 ( 1714) hydrogen bonds : angle 4.22152 ( 5142) metal coordination : bond 0.03887 ( 36) metal coordination : angle 28.89920 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 527 time to evaluate : 1.716 Fit side-chains REVERT: G 428 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8530 (ptpp) REVERT: G 874 GLU cc_start: 0.7964 (pt0) cc_final: 0.7658 (pt0) REVERT: G 903 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: B 197 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: I 153 MET cc_start: 0.8758 (mmt) cc_final: 0.8498 (mmm) REVERT: H 36 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: A 81 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: A 124 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: L 51 ASP cc_start: 0.8488 (t70) cc_final: 0.8076 (t0) REVERT: M 209 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: M 456 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: M 462 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8536 (tm) REVERT: K 87 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: J 69 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8953 (m-80) outliers start: 97 outliers final: 48 residues processed: 595 average time/residue: 0.8893 time to fit residues: 627.6824 Evaluate side-chains 573 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 514 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 109 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 367 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 375 optimal weight: 4.9990 chunk 107 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 22 GLN F 237 GLN F 238 ASN G 218 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 285 ASN K 27 ASN K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.082273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.064265 restraints weight = 30307.963| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 0.85 r_work: 0.2670 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38783 Z= 0.438 Angle : 2.485 50.479 52611 Z= 1.431 Chirality : 0.452 6.708 5838 Planarity : 0.005 0.064 6552 Dihedral : 9.566 104.664 5854 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 2.73 % Allowed : 15.06 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.40 (0.12), residues: 4710 helix: 1.63 (0.10), residues: 2736 sheet: 0.25 (0.31), residues: 298 loop : -0.00 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 90 TYR 0.021 0.002 TYR H 242 PHE 0.028 0.002 PHE L 341 TRP 0.018 0.002 TRP L 143 HIS 0.009 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01210 (38747) covalent geometry : angle 2.17553 (52518) hydrogen bonds : bond 0.07359 ( 1714) hydrogen bonds : angle 4.52510 ( 5142) metal coordination : bond 0.05685 ( 36) metal coordination : angle 28.66666 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 524 time to evaluate : 1.737 Fit side-chains REVERT: F 252 PHE cc_start: 0.9641 (OUTLIER) cc_final: 0.9315 (m-80) REVERT: E 90 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8172 (mtt90) REVERT: G 428 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8618 (ptpp) REVERT: G 806 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: G 874 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: G 903 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: C 490 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: I 153 MET cc_start: 0.8781 (mmt) cc_final: 0.8521 (mmm) REVERT: H 32 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7675 (tmm) REVERT: H 36 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: A 81 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: M 209 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: M 447 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8485 (mppt) REVERT: M 456 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: M 462 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8579 (tm) REVERT: N 197 MET cc_start: 0.8182 (mmm) cc_final: 0.7961 (mmt) REVERT: K 87 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7821 (mtt-85) REVERT: J 69 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8495 (t80) outliers start: 106 outliers final: 54 residues processed: 594 average time/residue: 0.8854 time to fit residues: 623.2392 Evaluate side-chains 580 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 511 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 267 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 46 optimal weight: 8.9990 chunk 433 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 439 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 834 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.082683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.064486 restraints weight = 30256.656| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 0.89 r_work: 0.2675 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38783 Z= 0.421 Angle : 2.482 50.599 52611 Z= 1.429 Chirality : 0.450 6.716 5838 Planarity : 0.004 0.048 6552 Dihedral : 9.597 104.942 5852 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.68 % Allowed : 14.98 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.41 (0.12), residues: 4710 helix: 1.64 (0.10), residues: 2735 sheet: 0.24 (0.30), residues: 298 loop : -0.01 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 90 TYR 0.020 0.002 TYR H 242 PHE 0.028 0.002 PHE L 341 TRP 0.020 0.001 TRP L 143 HIS 0.008 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01179 (38747) covalent geometry : angle 2.17118 (52518) hydrogen bonds : bond 0.06980 ( 1714) hydrogen bonds : angle 4.49545 ( 5142) metal coordination : bond 0.05438 ( 36) metal coordination : angle 28.68910 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 517 time to evaluate : 1.635 Fit side-chains REVERT: F 252 PHE cc_start: 0.9642 (OUTLIER) cc_final: 0.9331 (m-80) REVERT: E 90 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8128 (mtt90) REVERT: E 110 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: G 428 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8629 (ptpp) REVERT: G 806 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: G 874 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: G 903 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: C 238 ASP cc_start: 0.8438 (t70) cc_final: 0.8202 (t70) REVERT: I 153 MET cc_start: 0.8776 (mmt) cc_final: 0.8524 (mmm) REVERT: H 36 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: H 218 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: A 81 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: L 476 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: M 209 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: M 447 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8514 (mppt) REVERT: M 456 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: M 462 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8581 (tm) REVERT: N 197 MET cc_start: 0.8164 (mmm) cc_final: 0.7941 (mmt) REVERT: K 87 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7793 (mtt-85) REVERT: J 69 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8497 (t80) outliers start: 104 outliers final: 54 residues processed: 584 average time/residue: 0.8917 time to fit residues: 619.0762 Evaluate side-chains 585 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 515 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 211 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 419 optimal weight: 30.0000 chunk 311 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 352 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 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 834 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS K 27 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.064891 restraints weight = 30339.470| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 0.85 r_work: 0.2685 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38783 Z= 0.416 Angle : 2.482 50.500 52611 Z= 1.429 Chirality : 0.449 6.650 5838 Planarity : 0.004 0.048 6552 Dihedral : 9.614 105.661 5850 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 2.58 % Allowed : 15.13 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.43 (0.12), residues: 4710 helix: 1.66 (0.10), residues: 2733 sheet: 0.24 (0.30), residues: 298 loop : -0.01 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 90 TYR 0.023 0.002 TYR H 242 PHE 0.028 0.002 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01170 (38747) covalent geometry : angle 2.17060 (52518) hydrogen bonds : bond 0.06870 ( 1714) hydrogen bonds : angle 4.48210 ( 5142) metal coordination : bond 0.05286 ( 36) metal coordination : angle 28.72887 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 521 time to evaluate : 1.600 Fit side-chains REVERT: F 252 PHE cc_start: 0.9640 (OUTLIER) cc_final: 0.9334 (m-80) REVERT: G 428 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8567 (ptpp) REVERT: G 806 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: G 903 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 238 ASP cc_start: 0.8433 (t70) cc_final: 0.8167 (t70) REVERT: C 490 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 220 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8134 (mp) REVERT: I 153 MET cc_start: 0.8772 (mmt) cc_final: 0.8514 (mmm) REVERT: H 218 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: A 81 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: L 529 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8066 (ttp-170) REVERT: M 26 LYS cc_start: 0.8975 (mttp) cc_final: 0.7885 (pttp) REVERT: M 456 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: M 462 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8583 (tm) REVERT: N 197 MET cc_start: 0.8157 (mmm) cc_final: 0.7938 (mmt) REVERT: K 87 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7783 (mtt-85) REVERT: J 69 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8493 (t80) REVERT: J 72 MET cc_start: 0.8724 (mtt) cc_final: 0.8414 (mtt) outliers start: 100 outliers final: 53 residues processed: 583 average time/residue: 0.8594 time to fit residues: 594.3748 Evaluate side-chains 582 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 516 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 529 ARG Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 267 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 453 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 260 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 390 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 834 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 285 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.067938 restraints weight = 31020.603| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 0.86 r_work: 0.2758 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38783 Z= 0.384 Angle : 2.477 50.644 52611 Z= 1.425 Chirality : 0.442 6.484 5838 Planarity : 0.004 0.067 6552 Dihedral : 9.132 106.208 5850 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 1.80 % Allowed : 16.06 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.58 (0.12), residues: 4710 helix: 1.82 (0.10), residues: 2742 sheet: 0.24 (0.30), residues: 298 loop : -0.02 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 90 TYR 0.027 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.005 0.001 HIS N 368 Details of bonding type rmsd covalent geometry : bond 0.01120 (38747) covalent geometry : angle 2.15821 (52518) hydrogen bonds : bond 0.05411 ( 1714) hydrogen bonds : angle 4.23173 ( 5142) metal coordination : bond 0.03514 ( 36) metal coordination : angle 28.99707 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 522 time to evaluate : 1.925 Fit side-chains REVERT: E 90 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8121 (mtt90) REVERT: G 428 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8472 (ptpp) REVERT: G 903 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: C 238 ASP cc_start: 0.8408 (t70) cc_final: 0.8163 (t70) REVERT: B 220 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7916 (mp) REVERT: I 153 MET cc_start: 0.8734 (mmt) cc_final: 0.8494 (mmm) REVERT: M 26 LYS cc_start: 0.8958 (mttp) cc_final: 0.7864 (pttt) REVERT: M 456 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: M 462 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8546 (tm) REVERT: K 87 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7740 (mtt-85) REVERT: J 69 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8919 (m-80) outliers start: 70 outliers final: 36 residues processed: 569 average time/residue: 0.8904 time to fit residues: 601.0990 Evaluate side-chains 552 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 509 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 92 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 368 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 462 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 358 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS K 27 ASN K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.067622 restraints weight = 30808.405| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 0.86 r_work: 0.2750 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38783 Z= 0.387 Angle : 2.476 50.602 52611 Z= 1.425 Chirality : 0.443 6.528 5838 Planarity : 0.004 0.051 6552 Dihedral : 8.976 105.575 5849 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 1.26 % Allowed : 16.81 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.63 (0.12), residues: 4710 helix: 1.87 (0.10), residues: 2724 sheet: 0.31 (0.30), residues: 299 loop : -0.00 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 90 TYR 0.024 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01124 (38747) covalent geometry : angle 2.15958 (52518) hydrogen bonds : bond 0.05560 ( 1714) hydrogen bonds : angle 4.21174 ( 5142) metal coordination : bond 0.03936 ( 36) metal coordination : angle 28.90564 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 511 time to evaluate : 1.538 Fit side-chains REVERT: F 252 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.9306 (m-80) REVERT: E 90 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8078 (mtt90) REVERT: G 428 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8452 (ptpp) REVERT: G 903 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 220 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7909 (mp) REVERT: I 153 MET cc_start: 0.8745 (mmt) cc_final: 0.8482 (mmm) REVERT: M 26 LYS cc_start: 0.8958 (mttp) cc_final: 0.7863 (pttt) REVERT: M 462 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8559 (tm) REVERT: K 87 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: J 69 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (m-80) outliers start: 49 outliers final: 36 residues processed: 547 average time/residue: 0.8728 time to fit residues: 566.5259 Evaluate side-chains 550 residues out of total 3882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 507 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 428 LYS Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 903 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 395 optimal weight: 9.9990 chunk 398 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 462 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 469 ASN G 490 GLN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS M 441 HIS K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065472 restraints weight = 30682.140| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 0.90 r_work: 0.2698 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38783 Z= 0.405 Angle : 2.481 50.537 52611 Z= 1.428 Chirality : 0.447 6.591 5838 Planarity : 0.004 0.053 6552 Dihedral : 9.197 105.490 5848 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 1.55 % Allowed : 16.65 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 1.55 (0.12), residues: 4710 helix: 1.77 (0.10), residues: 2737 sheet: 0.29 (0.30), residues: 299 loop : 0.02 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 90 TYR 0.021 0.002 TYR H 242 PHE 0.027 0.002 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01152 (38747) covalent geometry : angle 2.16756 (52518) hydrogen bonds : bond 0.06426 ( 1714) hydrogen bonds : angle 4.36865 ( 5142) metal coordination : bond 0.04864 ( 36) metal coordination : angle 28.78422 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24644.21 seconds wall clock time: 417 minutes 31.51 seconds (25051.51 seconds total)