Starting phenix.real_space_refine on Mon Jul 6 16:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7j_13237/07_2026/7p7j_13237.cif" } resolution = 2.7 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= 0.020 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 13 5.49 5 S 267 5.16 5 C 24392 2.51 5 N 6169 2.21 5 O 6574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37448 Number of models: 1 Model: "" Number of chains: 24 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: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4712 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 546} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1553 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4563 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} 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: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1199 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'DCQ': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "H" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "L" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 230 Unusual residues: {'3PE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.861 60.180 195.159 1.00 24.55 S ATOM 2741 SG CYS F 357 75.323 59.897 199.525 1.00 35.82 S ATOM 3062 SG CYS F 398 69.602 56.378 200.117 1.00 24.99 S ATOM 2697 SG CYS F 351 74.127 53.931 196.544 1.00 30.26 S ATOM 4054 SG CYS E 92 82.759 52.229 216.240 1.00 63.33 S ATOM 4088 SG CYS E 97 82.908 53.057 219.711 1.00 62.82 S ATOM 4366 SG CYS E 133 77.634 51.606 215.849 1.00 72.20 S ATOM 4392 SG CYS E 137 76.762 52.331 219.124 1.00 75.45 S ATOM 5476 SG CYS G 114 82.216 66.267 177.570 1.00 15.77 S ATOM 5416 SG CYS G 105 87.339 70.222 179.098 1.00 27.04 S ATOM 5436 SG CYS G 108 88.241 64.206 176.887 1.00 10.56 S ATOM 5830 SG CYS G 156 76.614 58.302 182.582 1.00 11.61 S ATOM 5811 SG CYS G 153 82.489 57.530 185.704 1.00 9.61 S ATOM 5859 SG CYS G 159 79.823 52.770 182.269 1.00 14.53 S ATOM 6203 SG CYS G 203 81.799 57.982 179.050 1.00 7.25 S ATOM 6428 SG CYS G 230 78.771 49.043 158.108 1.00 15.13 S ATOM 6713 SG CYS G 265 78.784 45.343 163.558 1.00 16.49 S ATOM 6476 SG CYS G 237 73.440 48.669 161.221 1.00 17.22 S ATOM 6452 SG CYS G 233 75.759 43.282 158.353 1.00 20.84 S ATOM 4877 SG CYS G 36 70.150 59.205 185.375 1.00 21.02 S ATOM 4953 SG CYS G 47 71.725 62.551 185.623 1.00 11.90 S ATOM 4979 SG CYS G 50 65.802 64.074 185.501 1.00 21.85 S ATOM 5128 SG CYS G 69 65.536 60.420 185.202 1.00 23.26 S ATOM 17192 SG CYS B 129 91.846 93.190 153.179 1.00 17.49 S ATOM 16689 SG CYS B 64 96.949 97.087 154.735 1.00 18.07 S ATOM 16683 SG CYS B 63 91.382 99.078 156.620 1.00 16.11 S ATOM 17409 SG CYS B 158 93.600 93.281 158.942 1.00 20.57 S ATOM 18740 SG CYS I 102 92.475 87.564 165.200 1.00 13.47 S ATOM 18715 SG CYS I 99 98.040 86.365 161.575 1.00 2.14 S ATOM 18758 SG CYS I 105 96.702 83.162 167.069 1.00 17.38 S ATOM 18473 SG CYS I 70 92.891 82.223 161.900 1.00 3.46 S ATOM 18787 SG CYS I 109 97.820 77.855 173.392 1.00 5.17 S ATOM 18450 SG CYS I 66 95.889 77.007 167.339 1.00 7.30 S ATOM 18410 SG CYS I 60 100.126 72.798 169.686 1.00 14.03 S ATOM 18428 SG CYS I 63 93.818 73.197 172.094 1.00 3.79 S Time building chain proxies: 7.56, per 1000 atoms: 0.20 Number of scatterers: 37448 At special positions: 0 Unit cell: (155.82, 210.94, 246.98, 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 13 15.00 O 6574 8.00 N 6169 7.00 C 24392 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 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: 4.773A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.573A 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: 4.431A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.830A 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: 5.084A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.236A 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: 4.943A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.584A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.739A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.289A 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: 4.707A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.275A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.775A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.713A 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: 4.512A 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: 4.400A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.932A 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: 4.408A 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: 4.974A 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: 4.922A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.477A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.046A 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: 4.432A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.575A 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 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: 5.767A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1716 hydrogen bonds defined for protein. 5148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 4.01 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: 15914 1.42 - 1.64: 21961 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38376 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" O13 3PE H 403 " pdb=" P 3PE H 403 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" O13 3PE A 202 " pdb=" P 3PE A 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" O13 3PE M 701 " pdb=" P 3PE M 701 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" O13 3PE I 203 " pdb=" P 3PE I 203 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.71e+00 ... (remaining 38371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 51401 2.82 - 5.63: 514 5.63 - 8.45: 99 8.45 - 11.27: 22 11.27 - 14.08: 4 Bond angle restraints: 52040 Sorted by residual: angle pdb=" CA PRO N 483 " pdb=" N PRO N 483 " pdb=" CD PRO N 483 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.51e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.15 12.66 2.21e+00 2.05e-01 3.28e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 126.78 -14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 132.31 -10.51 2.44e+00 1.68e-01 1.86e+01 ... (remaining 52035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 21846 33.84 - 67.68: 595 67.68 - 101.52: 28 101.52 - 135.36: 0 135.36 - 169.20: 1 Dihedral angle restraints: 22470 sinusoidal: 8991 harmonic: 13479 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 134.71 45.29 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 144.66 35.34 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.39 169.20 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5772 4.238 - 8.475: 0 8.475 - 12.713: 0 12.713 - 16.951: 0 16.951 - 21.188: 28 Chirality restraints: 5800 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 10.63 -21.19 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 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5797 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.004 2.00e-02 2.50e+03 2.38e-02 1.70e+01 pdb=" C1M DCQ B 302 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " -0.012 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " -0.036 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " 0.060 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.016 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET N 482 " 0.068 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO N 483 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO N 483 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 483 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 86 " -0.296 9.50e-02 1.11e+02 1.33e-01 1.20e+01 pdb=" NE ARG K 86 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG K 86 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG K 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 86 " -0.004 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4091 2.75 - 3.29: 36705 3.29 - 3.82: 69076 3.82 - 4.36: 83572 4.36 - 4.90: 139861 Nonbonded interactions: 333305 Sorted by model distance: nonbonded pdb=" OE1 GLU H 36 " pdb=" OH TYR H 242 " model vdw 2.212 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 116 " pdb=" OE2 GLU N 104 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.276 3.040 ... (remaining 333300 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.920 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 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 : 0.005 0.151 38412 Z= 0.232 Angle : 0.788 14.084 52133 Z= 0.394 Chirality : 1.468 21.188 5800 Planarity : 0.006 0.133 6496 Dihedral : 14.695 169.205 13848 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.25 % Allowed : 14.71 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.11), residues: 4677 helix: 0.37 (0.09), residues: 2705 sheet: -0.58 (0.29), residues: 298 loop : -0.88 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 727 TYR 0.036 0.002 TYR H 242 PHE 0.037 0.002 PHE L 341 TRP 0.021 0.001 TRP N 53 HIS 0.005 0.001 HIS F 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (38376) covalent geometry : angle 0.76892 / 0.39 (52040) hydrogen bonds : bond 0.05710 / 3.89 ( 1716) hydrogen bonds : angle 4.63523 / 3.32 ( 5148) metal coordination : bond 0.05539 / 3.63 ( 36) metal coordination : angle 4.10426 / 2.62 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 435 time to evaluate : 1.457 Fit side-chains REVERT: F 80 GLU cc_start: 0.7891 (tp30) cc_final: 0.7584 (tp30) REVERT: F 126 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8586 (p90) REVERT: E 86 ARG cc_start: 0.9147 (mtp-110) cc_final: 0.8938 (mtm-85) REVERT: E 125 ARG cc_start: 0.8561 (tmt90) cc_final: 0.8132 (tpt-90) REVERT: G 411 LYS cc_start: 0.9072 (mmpt) cc_final: 0.8563 (mppt) REVERT: G 874 GLU cc_start: 0.8545 (tp30) cc_final: 0.8318 (tt0) REVERT: C 202 GLU cc_start: 0.8022 (mp0) cc_final: 0.7820 (pp20) REVERT: C 285 MET cc_start: 0.9200 (tpp) cc_final: 0.8939 (tpp) REVERT: L 111 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: L 578 PHE cc_start: 0.7520 (m-10) cc_final: 0.6870 (t80) REVERT: M 466 PHE cc_start: 0.8245 (m-10) cc_final: 0.7522 (t80) REVERT: N 74 MET cc_start: 0.9054 (mtp) cc_final: 0.8849 (mtt) REVERT: J 85 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7576 (ttm110) outliers start: 48 outliers final: 33 residues processed: 476 average time/residue: 0.7572 time to fit residues: 430.7677 Evaluate side-chains 452 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 417 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 106 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 299 GLN G 310 GLN G 490 GLN G 583 ASN G 828 GLN C 359 HIS B 116 GLN H 45 ASN H 170 GLN H 192 GLN H 312 ASN L 360 GLN M 64 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.063451 restraints weight = 53588.793| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.41 r_work: 0.2783 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.267 38412 Z= 0.392 Angle : 2.490 56.370 52133 Z= 1.432 Chirality : 0.442 6.518 5800 Planarity : 0.004 0.068 6496 Dihedral : 7.270 168.832 5575 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Rotamer: Outliers : 1.98 % Allowed : 13.62 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 4677 helix: 1.16 (0.10), residues: 2693 sheet: -0.43 (0.30), residues: 289 loop : -0.66 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 529 TYR 0.022 0.001 TYR L 428 PHE 0.028 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.39 (38376) covalent geometry : angle 2.16944 / 1.43 (52040) hydrogen bonds : bond 0.04736 / 3.22 ( 1716) hydrogen bonds : angle 4.14225 / 2.98 ( 5148) metal coordination : bond 0.04734 / 3.11 ( 36) metal coordination : angle 29.03116 / 19.38 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 448 time to evaluate : 1.493 Fit side-chains REVERT: F 80 GLU cc_start: 0.8209 (tp30) cc_final: 0.7783 (tp30) REVERT: F 95 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6426 (tp30) REVERT: E 125 ARG cc_start: 0.8483 (tmt90) cc_final: 0.8114 (tpt-90) REVERT: E 126 PHE cc_start: 0.9081 (m-80) cc_final: 0.8797 (m-80) REVERT: G 874 GLU cc_start: 0.8156 (tp30) cc_final: 0.7895 (tt0) REVERT: C 285 MET cc_start: 0.9163 (tpp) cc_final: 0.8712 (tpp) REVERT: C 487 ASN cc_start: 0.7753 (t0) cc_final: 0.7501 (m110) REVERT: B 43 ASN cc_start: 0.8905 (t0) cc_final: 0.8487 (t0) REVERT: I 153 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: H 32 MET cc_start: 0.6319 (mtt) cc_final: 0.6113 (mtm) REVERT: H 241 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: L 111 GLU cc_start: 0.8239 (pt0) cc_final: 0.7787 (pm20) REVERT: L 578 PHE cc_start: 0.7148 (m-10) cc_final: 0.6750 (t80) REVERT: M 34 ILE cc_start: 0.8762 (pp) cc_final: 0.8493 (mp) REVERT: M 259 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8722 (mp) REVERT: M 291 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8514 (mtm) REVERT: M 466 PHE cc_start: 0.7830 (m-10) cc_final: 0.7331 (t80) REVERT: N 74 MET cc_start: 0.8936 (mtp) cc_final: 0.8648 (mtt) REVERT: N 104 GLU cc_start: 0.8824 (mp0) cc_final: 0.8622 (mp0) REVERT: J 85 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7323 (ttm110) outliers start: 76 outliers final: 28 residues processed: 503 average time/residue: 0.7472 time to fit residues: 449.5160 Evaluate side-chains 459 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 426 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 318 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 339 optimal weight: 7.9990 chunk 448 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 116 optimal weight: 0.0170 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 490 GLN G 583 ASN G 655 HIS B 116 GLN H 45 ASN H 170 GLN L 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.061339 restraints weight = 53289.540| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.39 r_work: 0.2732 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38412 Z= 0.406 Angle : 2.488 51.794 52133 Z= 1.432 Chirality : 0.447 6.596 5800 Planarity : 0.004 0.067 6496 Dihedral : 7.174 169.174 5547 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.26 % Allowed : 12.99 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.12), residues: 4677 helix: 1.39 (0.10), residues: 2715 sheet: -0.24 (0.31), residues: 281 loop : -0.49 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 40 TYR 0.026 0.002 TYR H 242 PHE 0.027 0.002 PHE L 341 TRP 0.015 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.40 (38376) covalent geometry : angle 2.17132 / 1.43 (52040) hydrogen bonds : bond 0.05232 / 3.57 ( 1716) hydrogen bonds : angle 4.16470 / 2.99 ( 5148) metal coordination : bond 0.04708 / 3.06 ( 36) metal coordination : angle 28.84407 / 19.29 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 445 time to evaluate : 1.353 Fit side-chains REVERT: F 80 GLU cc_start: 0.8300 (tp30) cc_final: 0.7882 (tp30) REVERT: F 95 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6384 (tp30) REVERT: F 307 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8307 (mp) REVERT: E 116 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8673 (tmtm) REVERT: E 125 ARG cc_start: 0.8545 (tmt90) cc_final: 0.8114 (tpt-90) REVERT: G 85 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: G 626 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: G 874 GLU cc_start: 0.8199 (tp30) cc_final: 0.7940 (tt0) REVERT: C 285 MET cc_start: 0.9218 (tpp) cc_final: 0.8814 (tpp) REVERT: C 487 ASN cc_start: 0.7766 (t0) cc_final: 0.7531 (m110) REVERT: B 43 ASN cc_start: 0.8943 (t0) cc_final: 0.8480 (t0) REVERT: I 153 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.6894 (mtt) REVERT: H 241 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: H 298 MET cc_start: 0.8473 (mtm) cc_final: 0.8239 (mmm) REVERT: A 125 TRP cc_start: 0.7060 (t-100) cc_final: 0.6835 (t-100) REVERT: L 111 GLU cc_start: 0.8247 (pt0) cc_final: 0.7803 (pm20) REVERT: L 578 PHE cc_start: 0.7061 (m-10) cc_final: 0.6794 (t80) REVERT: M 259 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8746 (mp) REVERT: M 291 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: M 466 PHE cc_start: 0.7850 (m-10) cc_final: 0.7383 (t80) REVERT: N 74 MET cc_start: 0.8940 (mtp) cc_final: 0.8611 (mtt) REVERT: J 85 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7398 (ttm110) outliers start: 87 outliers final: 40 residues processed: 502 average time/residue: 0.7552 time to fit residues: 452.4851 Evaluate side-chains 473 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 425 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 371 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 448 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 232 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 451 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN G 655 HIS B 116 GLN H 45 ASN H 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061676 restraints weight = 53072.500| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.40 r_work: 0.2739 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38412 Z= 0.396 Angle : 2.487 51.485 52133 Z= 1.431 Chirality : 0.445 6.544 5800 Planarity : 0.004 0.069 6496 Dihedral : 7.124 169.145 5542 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.36 % Allowed : 13.23 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4677 helix: 1.53 (0.10), residues: 2715 sheet: -0.12 (0.31), residues: 280 loop : -0.41 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 529 TYR 0.024 0.002 TYR H 242 PHE 0.026 0.001 PHE L 341 TRP 0.016 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.39 (38376) covalent geometry : angle 2.16890 / 1.43 (52040) hydrogen bonds : bond 0.05032 / 3.43 ( 1716) hydrogen bonds : angle 4.11950 / 2.96 ( 5148) metal coordination : bond 0.03904 / 2.51 ( 36) metal coordination : angle 28.90215 / 19.30 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 439 time to evaluate : 1.463 Fit side-chains REVERT: F 80 GLU cc_start: 0.8324 (tp30) cc_final: 0.7876 (tp30) REVERT: F 95 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6292 (tp30) REVERT: F 307 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8279 (mp) REVERT: E 114 ASN cc_start: 0.8939 (t0) cc_final: 0.8734 (t0) REVERT: E 116 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8669 (tmtm) REVERT: E 125 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8162 (tpt-90) REVERT: E 126 PHE cc_start: 0.9027 (m-80) cc_final: 0.8824 (m-80) REVERT: G 85 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: G 411 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8515 (mppt) REVERT: G 874 GLU cc_start: 0.8203 (tp30) cc_final: 0.7954 (tt0) REVERT: C 62 ASP cc_start: 0.8821 (t70) cc_final: 0.8574 (t0) REVERT: C 285 MET cc_start: 0.9194 (tpp) cc_final: 0.8794 (tpp) REVERT: B 43 ASN cc_start: 0.8944 (t0) cc_final: 0.8477 (t0) REVERT: B 68 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8588 (ttm) REVERT: I 153 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: H 241 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: A 125 TRP cc_start: 0.7079 (t-100) cc_final: 0.6818 (t-100) REVERT: L 13 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8829 (mp) REVERT: L 569 MET cc_start: 0.9139 (mmm) cc_final: 0.8888 (mmm) REVERT: L 578 PHE cc_start: 0.7057 (m-10) cc_final: 0.6784 (t80) REVERT: M 259 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8705 (mp) REVERT: M 291 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: M 466 PHE cc_start: 0.7852 (m-10) cc_final: 0.7382 (t80) REVERT: N 74 MET cc_start: 0.8933 (mtp) cc_final: 0.8589 (mtt) REVERT: N 102 LYS cc_start: 0.8931 (mttm) cc_final: 0.8705 (mttm) REVERT: J 85 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7556 (ttm-80) outliers start: 91 outliers final: 43 residues processed: 501 average time/residue: 0.7401 time to fit residues: 445.7147 Evaluate side-chains 479 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 426 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 75 optimal weight: 7.9990 chunk 409 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN G 655 HIS B 116 GLN H 170 GLN L 163 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.061752 restraints weight = 53107.848| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.40 r_work: 0.2742 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38412 Z= 0.394 Angle : 2.488 51.007 52133 Z= 1.431 Chirality : 0.445 6.535 5800 Planarity : 0.004 0.070 6496 Dihedral : 7.089 169.195 5540 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 13.51 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 4677 helix: 1.61 (0.10), residues: 2715 sheet: -0.05 (0.31), residues: 280 loop : -0.35 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 529 TYR 0.024 0.002 TYR H 242 PHE 0.026 0.001 PHE L 341 TRP 0.016 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.39 (38376) covalent geometry : angle 2.16897 / 1.43 (52040) hydrogen bonds : bond 0.04984 / 3.40 ( 1716) hydrogen bonds : angle 4.09666 / 2.95 ( 5148) metal coordination : bond 0.03702 / 2.38 ( 36) metal coordination : angle 28.92174 / 19.31 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 441 time to evaluate : 1.512 Fit side-chains REVERT: F 80 GLU cc_start: 0.8320 (tp30) cc_final: 0.7868 (tp30) REVERT: F 95 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6234 (tp30) REVERT: F 307 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (mp) REVERT: E 114 ASN cc_start: 0.9037 (t0) cc_final: 0.8820 (t0) REVERT: E 116 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8682 (tptt) REVERT: E 125 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8096 (tpt-90) REVERT: E 126 PHE cc_start: 0.8971 (m-80) cc_final: 0.8713 (m-80) REVERT: G 85 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: G 287 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7879 (mmm-85) REVERT: G 411 LYS cc_start: 0.9031 (mmpt) cc_final: 0.8502 (mppt) REVERT: G 874 GLU cc_start: 0.8203 (tp30) cc_final: 0.7945 (tt0) REVERT: C 62 ASP cc_start: 0.8823 (t70) cc_final: 0.8575 (t0) REVERT: C 285 MET cc_start: 0.9198 (tpp) cc_final: 0.8794 (tpp) REVERT: B 43 ASN cc_start: 0.8940 (t0) cc_final: 0.8463 (t0) REVERT: I 27 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8371 (ttpt) REVERT: I 153 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.6877 (mtt) REVERT: H 252 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8548 (ttp) REVERT: L 569 MET cc_start: 0.9148 (mmm) cc_final: 0.8887 (mmm) REVERT: L 578 PHE cc_start: 0.7052 (m-10) cc_final: 0.6780 (t80) REVERT: M 259 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8690 (mt) REVERT: M 291 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8453 (mtm) REVERT: M 466 PHE cc_start: 0.7842 (m-10) cc_final: 0.7379 (t80) REVERT: N 74 MET cc_start: 0.8904 (mtp) cc_final: 0.8537 (mtt) REVERT: N 102 LYS cc_start: 0.8908 (mttm) cc_final: 0.8668 (mttm) REVERT: J 23 THR cc_start: 0.9221 (m) cc_final: 0.8939 (m) REVERT: J 85 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7530 (ttm-80) outliers start: 88 outliers final: 42 residues processed: 501 average time/residue: 0.7606 time to fit residues: 458.8025 Evaluate side-chains 481 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 430 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 462 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 182 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 357 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 428 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 277 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 110 HIS F 386 GLN G 88 GLN G 490 GLN G 583 ASN B 116 GLN H 45 ASN H 170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.060906 restraints weight = 53008.774| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.39 r_work: 0.2722 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38412 Z= 0.409 Angle : 2.491 50.809 52133 Z= 1.433 Chirality : 0.446 6.597 5800 Planarity : 0.004 0.069 6496 Dihedral : 7.206 169.027 5540 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.39 % Allowed : 13.72 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4677 helix: 1.58 (0.10), residues: 2711 sheet: -0.04 (0.31), residues: 280 loop : -0.33 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 63 TYR 0.025 0.002 TYR H 242 PHE 0.026 0.002 PHE L 341 TRP 0.015 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.41 (38376) covalent geometry : angle 2.17496 / 1.43 (52040) hydrogen bonds : bond 0.05305 / 3.62 ( 1716) hydrogen bonds : angle 4.16198 / 2.99 ( 5148) metal coordination : bond 0.04178 / 2.73 ( 36) metal coordination : angle 28.85239 / 19.29 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 441 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: F 80 GLU cc_start: 0.8320 (tp30) cc_final: 0.7918 (tp30) REVERT: F 95 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6220 (tp30) REVERT: F 307 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 114 ASN cc_start: 0.9029 (t0) cc_final: 0.8821 (t0) REVERT: E 125 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7986 (tpt-90) REVERT: E 143 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8774 (ttm) REVERT: G 85 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: G 287 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7935 (mmm-85) REVERT: G 411 LYS cc_start: 0.9038 (mmpt) cc_final: 0.8527 (mppt) REVERT: G 626 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: G 874 GLU cc_start: 0.8213 (tp30) cc_final: 0.7960 (tt0) REVERT: C 62 ASP cc_start: 0.8842 (t70) cc_final: 0.8597 (t0) REVERT: C 285 MET cc_start: 0.9190 (tpp) cc_final: 0.8768 (tpp) REVERT: C 487 ASN cc_start: 0.7920 (t0) cc_final: 0.7664 (m110) REVERT: B 43 ASN cc_start: 0.8960 (t0) cc_final: 0.8472 (t0) REVERT: I 153 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: H 241 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: A 102 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8202 (mt-10) REVERT: L 578 PHE cc_start: 0.7077 (m-10) cc_final: 0.6781 (t80) REVERT: M 259 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8709 (mt) REVERT: M 291 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8458 (mtm) REVERT: M 466 PHE cc_start: 0.7841 (m-10) cc_final: 0.7397 (t80) REVERT: N 74 MET cc_start: 0.8916 (mtp) cc_final: 0.8542 (mtt) REVERT: N 102 LYS cc_start: 0.8943 (mttm) cc_final: 0.8725 (mttm) REVERT: J 23 THR cc_start: 0.9219 (m) cc_final: 0.8949 (m) outliers start: 92 outliers final: 44 residues processed: 500 average time/residue: 0.7423 time to fit residues: 446.2702 Evaluate side-chains 477 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 423 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 445 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 345 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN B 116 GLN H 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.060926 restraints weight = 53048.432| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.39 r_work: 0.2722 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38412 Z= 0.406 Angle : 2.493 50.792 52133 Z= 1.434 Chirality : 0.446 6.582 5800 Planarity : 0.004 0.070 6496 Dihedral : 7.256 168.931 5539 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 14.16 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 4677 helix: 1.58 (0.10), residues: 2711 sheet: -0.04 (0.31), residues: 283 loop : -0.32 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 529 TYR 0.026 0.002 TYR H 242 PHE 0.026 0.002 PHE L 341 TRP 0.016 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.40 (38376) covalent geometry : angle 2.17648 / 1.43 (52040) hydrogen bonds : bond 0.05295 / 3.62 ( 1716) hydrogen bonds : angle 4.17534 / 3.00 ( 5148) metal coordination : bond 0.04040 / 2.62 ( 36) metal coordination : angle 28.88729 / 19.31 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 435 time to evaluate : 1.494 Fit side-chains REVERT: F 95 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: F 307 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8385 (mp) REVERT: E 114 ASN cc_start: 0.9091 (t0) cc_final: 0.8877 (t0) REVERT: E 125 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8048 (tpt-90) REVERT: E 126 PHE cc_start: 0.9030 (m-80) cc_final: 0.8634 (m-80) REVERT: G 85 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: G 287 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7875 (mmm-85) REVERT: G 626 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: G 837 MET cc_start: 0.6981 (ttt) cc_final: 0.6540 (ttt) REVERT: G 874 GLU cc_start: 0.8215 (tp30) cc_final: 0.7962 (tt0) REVERT: C 62 ASP cc_start: 0.8857 (t70) cc_final: 0.8609 (t0) REVERT: C 285 MET cc_start: 0.9188 (tpp) cc_final: 0.8767 (tpp) REVERT: C 333 MET cc_start: 0.8162 (mtm) cc_final: 0.7492 (mmm) REVERT: C 487 ASN cc_start: 0.8062 (t0) cc_final: 0.7696 (m110) REVERT: B 43 ASN cc_start: 0.8960 (t0) cc_final: 0.8478 (t0) REVERT: I 153 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.6923 (mtt) REVERT: H 32 MET cc_start: 0.6488 (mtm) cc_final: 0.5823 (ttp) REVERT: H 241 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: A 102 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8225 (mt-10) REVERT: L 578 PHE cc_start: 0.7046 (m-10) cc_final: 0.6759 (t80) REVERT: M 259 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8735 (mt) REVERT: M 291 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: M 364 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: M 466 PHE cc_start: 0.7860 (m-10) cc_final: 0.7401 (t80) REVERT: N 74 MET cc_start: 0.8899 (mtp) cc_final: 0.8507 (mtt) REVERT: N 102 LYS cc_start: 0.8945 (mttm) cc_final: 0.8718 (mttm) REVERT: K 26 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8401 (mtm-85) REVERT: J 23 THR cc_start: 0.9204 (m) cc_final: 0.8953 (m) REVERT: J 85 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7623 (ttm-80) outliers start: 87 outliers final: 50 residues processed: 495 average time/residue: 0.7633 time to fit residues: 452.7333 Evaluate side-chains 483 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 291 ARG Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 155 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 338 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 387 optimal weight: 10.0000 chunk 207 optimal weight: 0.0670 overall best weight: 1.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN B 116 GLN H 45 ASN H 113 ASN H 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062869 restraints weight = 53154.189| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.40 r_work: 0.2768 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38412 Z= 0.385 Angle : 2.492 51.834 52133 Z= 1.432 Chirality : 0.442 6.460 5800 Planarity : 0.004 0.071 6496 Dihedral : 7.026 169.081 5539 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.92 % Allowed : 14.60 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 4677 helix: 1.71 (0.10), residues: 2707 sheet: 0.07 (0.31), residues: 290 loop : -0.30 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 63 TYR 0.026 0.001 TYR M 435 PHE 0.028 0.001 PHE C 183 TRP 0.019 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.38 (38376) covalent geometry : angle 2.17024 / 1.43 (52040) hydrogen bonds : bond 0.04595 / 3.13 ( 1716) hydrogen bonds : angle 4.02762 / 2.89 ( 5148) metal coordination : bond 0.02925 / 1.81 ( 36) metal coordination : angle 29.05935 / 19.35 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 442 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: F 95 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: E 125 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8062 (tpt-90) REVERT: E 126 PHE cc_start: 0.8915 (m-80) cc_final: 0.8544 (m-80) REVERT: G 287 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: G 411 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8522 (mppt) REVERT: G 837 MET cc_start: 0.7048 (ttt) cc_final: 0.6496 (ttt) REVERT: G 874 GLU cc_start: 0.8195 (tp30) cc_final: 0.7937 (tt0) REVERT: C 62 ASP cc_start: 0.8818 (t70) cc_final: 0.8562 (t0) REVERT: C 285 MET cc_start: 0.9172 (tpp) cc_final: 0.8770 (tpp) REVERT: C 333 MET cc_start: 0.8066 (mtm) cc_final: 0.7453 (mmm) REVERT: B 4 THR cc_start: 0.7844 (t) cc_final: 0.7486 (p) REVERT: B 43 ASN cc_start: 0.8923 (t0) cc_final: 0.8450 (t0) REVERT: I 153 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.6877 (mtt) REVERT: H 241 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: H 298 MET cc_start: 0.8532 (mtm) cc_final: 0.8321 (mmm) REVERT: A 102 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 116 TYR cc_start: 0.9315 (t80) cc_final: 0.9085 (t80) REVERT: L 578 PHE cc_start: 0.7025 (m-10) cc_final: 0.6745 (t80) REVERT: M 259 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8652 (mt) REVERT: M 466 PHE cc_start: 0.7831 (m-10) cc_final: 0.7370 (t80) REVERT: N 74 MET cc_start: 0.8871 (mtp) cc_final: 0.8458 (mtt) REVERT: N 102 LYS cc_start: 0.8900 (mttm) cc_final: 0.8677 (mttm) REVERT: K 26 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8354 (mtm-85) REVERT: J 23 THR cc_start: 0.9196 (m) cc_final: 0.8959 (m) outliers start: 74 outliers final: 42 residues processed: 497 average time/residue: 0.7632 time to fit residues: 454.7562 Evaluate side-chains 477 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 429 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 355 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 449 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN G 828 GLN B 116 GLN H 170 GLN J 22 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060208 restraints weight = 53353.941| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.39 r_work: 0.2706 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38412 Z= 0.425 Angle : 2.501 50.827 52133 Z= 1.437 Chirality : 0.448 6.649 5800 Planarity : 0.004 0.066 6496 Dihedral : 7.385 169.311 5539 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 1.82 % Allowed : 14.81 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4677 helix: 1.58 (0.10), residues: 2707 sheet: -0.05 (0.31), residues: 286 loop : -0.26 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 86 TYR 0.027 0.002 TYR N 76 PHE 0.025 0.002 PHE L 341 TRP 0.012 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01191 / 0.42 (38376) covalent geometry : angle 2.18628 / 1.43 (52040) hydrogen bonds : bond 0.05662 / 3.87 ( 1716) hydrogen bonds : angle 4.21611 / 3.02 ( 5148) metal coordination : bond 0.04548 / 2.99 ( 36) metal coordination : angle 28.83348 / 19.31 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 431 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: F 95 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: E 125 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8122 (tpt-90) REVERT: G 287 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7918 (mmm-85) REVERT: G 414 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8614 (p0) REVERT: G 837 MET cc_start: 0.6975 (ttt) cc_final: 0.6355 (ttt) REVERT: G 874 GLU cc_start: 0.8231 (tp30) cc_final: 0.7980 (tt0) REVERT: C 62 ASP cc_start: 0.8869 (t70) cc_final: 0.8626 (t0) REVERT: C 285 MET cc_start: 0.9211 (tpp) cc_final: 0.8763 (tpp) REVERT: C 333 MET cc_start: 0.8195 (mtm) cc_final: 0.7580 (mmm) REVERT: C 487 ASN cc_start: 0.8072 (t0) cc_final: 0.7773 (m110) REVERT: B 4 THR cc_start: 0.7893 (t) cc_final: 0.7428 (p) REVERT: B 43 ASN cc_start: 0.8982 (t0) cc_final: 0.8497 (t0) REVERT: B 219 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8132 (mm-30) REVERT: I 153 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: H 241 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: A 102 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 116 TYR cc_start: 0.9349 (t80) cc_final: 0.9069 (t80) REVERT: L 214 MET cc_start: 0.8633 (mmt) cc_final: 0.8340 (mmt) REVERT: L 578 PHE cc_start: 0.7190 (m-10) cc_final: 0.6782 (t80) REVERT: M 34 ILE cc_start: 0.8726 (pp) cc_final: 0.8487 (mp) REVERT: M 259 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (mt) REVERT: M 466 PHE cc_start: 0.7905 (m-10) cc_final: 0.7430 (t80) REVERT: K 26 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8369 (mtm-85) REVERT: J 23 THR cc_start: 0.9198 (m) cc_final: 0.8925 (m) REVERT: J 85 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7591 (ttm-80) outliers start: 70 outliers final: 42 residues processed: 480 average time/residue: 0.7646 time to fit residues: 439.4708 Evaluate side-chains 471 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 422 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 160 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN B 116 GLN H 45 ASN H 170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.060456 restraints weight = 53092.525| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.38 r_work: 0.2711 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38412 Z= 0.418 Angle : 2.501 50.791 52133 Z= 1.437 Chirality : 0.447 6.616 5800 Planarity : 0.004 0.068 6496 Dihedral : 7.528 168.940 5537 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 15.18 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4677 helix: 1.56 (0.10), residues: 2704 sheet: -0.10 (0.31), residues: 281 loop : -0.29 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 63 TYR 0.028 0.002 TYR H 242 PHE 0.026 0.002 PHE C 183 TRP 0.015 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.42 (38376) covalent geometry : angle 2.18494 / 1.43 (52040) hydrogen bonds : bond 0.05555 / 3.80 ( 1716) hydrogen bonds : angle 4.22955 / 3.03 ( 5148) metal coordination : bond 0.04255 / 2.76 ( 36) metal coordination : angle 28.87990 / 19.34 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: F 95 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: E 116 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8705 (tmtm) REVERT: E 125 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8301 (tpt-90) REVERT: E 126 PHE cc_start: 0.8959 (m-80) cc_final: 0.8704 (m-80) REVERT: G 287 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7890 (mmm-85) REVERT: G 414 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8587 (p0) REVERT: G 837 MET cc_start: 0.6810 (ttt) cc_final: 0.6285 (ttt) REVERT: G 874 GLU cc_start: 0.8216 (tp30) cc_final: 0.7954 (tt0) REVERT: C 62 ASP cc_start: 0.8916 (t70) cc_final: 0.8662 (t0) REVERT: C 285 MET cc_start: 0.9210 (tpp) cc_final: 0.8776 (tpp) REVERT: C 333 MET cc_start: 0.8177 (mtm) cc_final: 0.7587 (mmm) REVERT: B 4 THR cc_start: 0.7889 (t) cc_final: 0.7430 (p) REVERT: B 43 ASN cc_start: 0.8974 (t0) cc_final: 0.8493 (t0) REVERT: I 153 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.6901 (mtt) REVERT: H 241 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: A 63 ARG cc_start: 0.7741 (tpp-160) cc_final: 0.7522 (tpp80) REVERT: A 102 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 116 TYR cc_start: 0.9330 (t80) cc_final: 0.9061 (t80) REVERT: L 578 PHE cc_start: 0.7344 (m-10) cc_final: 0.6874 (t80) REVERT: M 34 ILE cc_start: 0.8705 (pp) cc_final: 0.8436 (mp) REVERT: M 259 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8709 (mt) REVERT: M 466 PHE cc_start: 0.7962 (m-10) cc_final: 0.7501 (t80) REVERT: N 74 MET cc_start: 0.9006 (mtp) cc_final: 0.8613 (mtt) REVERT: K 26 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (mtm-85) REVERT: J 23 THR cc_start: 0.9188 (m) cc_final: 0.8941 (m) REVERT: J 85 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7705 (ttm-80) outliers start: 61 outliers final: 41 residues processed: 475 average time/residue: 0.7403 time to fit residues: 420.1627 Evaluate side-chains 471 residues out of total 3859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 423 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 192 optimal weight: 9.9990 chunk 420 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 427 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 461 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN B 116 GLN H 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.059811 restraints weight = 53105.225| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.38 r_work: 0.2695 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38412 Z= 0.433 Angle : 2.505 50.805 52133 Z= 1.439 Chirality : 0.448 6.662 5800 Planarity : 0.004 0.071 6496 Dihedral : 7.700 169.106 5537 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.46 % Allowed : 15.31 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4677 helix: 1.49 (0.10), residues: 2706 sheet: -0.14 (0.31), residues: 278 loop : -0.29 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 63 TYR 0.028 0.002 TYR H 242 PHE 0.025 0.002 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01208 / 0.43 (38376) covalent geometry : angle 2.19136 / 1.44 (52040) hydrogen bonds : bond 0.05905 / 4.05 ( 1716) hydrogen bonds : angle 4.30281 / 3.09 ( 5148) metal coordination : bond 0.04744 / 3.13 ( 36) metal coordination : angle 28.83651 / 19.34 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17533.66 seconds wall clock time: 297 minutes 53.21 seconds (17873.21 seconds total)