Starting phenix.real_space_refine on Fri Jan 16 15:05:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.map" model { file = "/net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p64_13217/01_2026/7p64_13217.cif" } resolution = 2.5 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= 0.022 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 21 5.49 5 S 267 5.16 5 C 24804 2.51 5 N 6209 2.21 5 O 7647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38981 Number of models: 1 Model: "" Number of chains: 37 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 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: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4741 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 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: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4637 Classifications: {'peptide': 606} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 203 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'3PE': 6, 'LFA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 308 Classifications: {'water': 308} Link IDs: {None: 307} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "N" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 74.768 60.483 191.847 1.00 24.98 S ATOM 2741 SG CYS F 357 78.331 59.905 196.082 1.00 36.60 S ATOM 3062 SG CYS F 398 72.463 56.706 196.813 1.00 36.25 S ATOM 2697 SG CYS F 351 76.688 54.054 193.052 1.00 27.68 S ATOM 4054 SG CYS E 92 86.138 51.990 212.373 1.00 49.60 S ATOM 4088 SG CYS E 97 86.467 52.779 215.849 1.00 48.93 S ATOM 4366 SG CYS E 133 80.921 51.435 212.287 1.00 61.55 S ATOM 4392 SG CYS E 137 80.270 52.235 215.519 1.00 55.26 S ATOM 5476 SG CYS G 114 84.532 66.081 173.721 1.00 12.78 S ATOM 5416 SG CYS G 105 89.900 69.832 174.931 1.00 22.30 S ATOM 5436 SG CYS G 108 90.372 63.731 172.785 1.00 13.38 S ATOM 5830 SG CYS G 156 78.797 58.403 178.993 1.00 19.56 S ATOM 5811 SG CYS G 153 84.756 57.223 181.848 1.00 15.18 S ATOM 5859 SG CYS G 159 81.699 52.688 178.472 1.00 10.59 S ATOM 6203 SG CYS G 203 83.744 57.824 175.205 1.00 17.86 S ATOM 6428 SG CYS G 230 79.449 49.183 154.321 1.00 17.83 S ATOM 6713 SG CYS G 265 79.571 45.456 159.722 1.00 22.05 S ATOM 6476 SG CYS G 237 74.237 49.006 157.683 1.00 15.82 S ATOM 6452 SG CYS G 233 76.239 43.527 154.696 1.00 18.02 S ATOM 4877 SG CYS G 36 72.526 59.622 182.093 1.00 17.78 S ATOM 4953 SG CYS G 47 74.192 62.990 182.347 1.00 15.20 S ATOM 4979 SG CYS G 50 68.484 64.735 182.485 1.00 24.91 S ATOM 5128 SG CYS G 69 67.813 61.174 182.147 1.00 22.83 S ATOM 17236 SG CYS B 129 94.279 92.696 149.025 1.00 17.56 S ATOM 16733 SG CYS B 64 99.640 96.389 150.368 1.00 20.91 S ATOM 16727 SG CYS B 63 94.173 98.583 152.435 1.00 21.43 S ATOM 17453 SG CYS B 158 96.320 92.688 154.669 1.00 25.28 S ATOM 18784 SG CYS I 102 95.258 86.992 160.916 1.00 12.93 S ATOM 18759 SG CYS I 99 100.546 85.585 157.048 1.00 17.28 S ATOM 18802 SG CYS I 105 99.258 82.363 162.594 1.00 19.91 S ATOM 18517 SG CYS I 70 95.171 81.678 157.588 1.00 18.18 S ATOM 18831 SG CYS I 109 100.424 76.964 168.913 1.00 15.95 S ATOM 18494 SG CYS I 66 98.211 76.194 162.887 1.00 26.03 S ATOM 18454 SG CYS I 60 102.312 71.830 165.027 1.00 20.25 S ATOM 18472 SG CYS I 63 96.179 72.556 167.801 1.00 18.36 S Time building chain proxies: 8.22, per 1000 atoms: 0.21 Number of scatterers: 38981 At special positions: 0 Unit cell: (158.5, 215, 243.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 21 15.00 O 7647 8.00 N 6209 7.00 C 24804 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 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="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " 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="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="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="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 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: 4.728A 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: 4.517A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.966A 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: 4.955A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.045A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for '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: 4.980A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.927A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.125A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.084A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.803A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.844A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.736A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.007A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.839A 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: 4.553A 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: 4.429A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 5.006A 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: 4.651A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.130A 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: 4.755A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.422A 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: 4.536A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.133A 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: 4.435A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.136A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.209A 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 1711 hydrogen bonds defined for protein. 5133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 4.54 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: 16008 1.42 - 1.64: 22411 1.64 - 1.86: 410 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38921 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" CB PRO C 201 " pdb=" CG PRO C 201 " ideal model delta sigma weight residual 1.492 1.684 -0.192 5.00e-02 4.00e+02 1.48e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.606 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O13 3PE L 702 " pdb=" P 3PE L 702 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.98e+00 ... (remaining 38916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 52248 3.36 - 6.72: 372 6.72 - 10.08: 46 10.08 - 13.44: 9 13.44 - 16.80: 2 Bond angle restraints: 52677 Sorted by residual: angle pdb=" CA PRO C 201 " pdb=" N PRO C 201 " pdb=" CD PRO C 201 " ideal model delta sigma weight residual 112.00 95.20 16.80 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 95.89 13.92 2.21e+00 2.05e-01 3.97e+01 angle pdb=" N PRO C 201 " pdb=" CD PRO C 201 " pdb=" CG PRO C 201 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.47e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 134.65 -12.85 2.44e+00 1.68e-01 2.77e+01 angle pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 52672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 21832 28.00 - 55.99: 1146 55.99 - 83.99: 114 83.99 - 111.99: 23 111.99 - 139.99: 6 Dihedral angle restraints: 23121 sinusoidal: 9608 harmonic: 13513 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 180.00 137.63 42.37 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.51 34.49 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 23118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5799 4.240 - 8.479: 0 8.479 - 12.719: 0 12.719 - 16.958: 0 16.958 - 21.198: 28 Chirality restraints: 5827 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 10.64 -21.20 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 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5824 not shown) Planarity restraints: 6535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.010 2.00e-02 2.50e+03 3.22e-02 3.11e+01 pdb=" C1M DCQ B 302 " -0.074 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " 0.007 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.036 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " 0.040 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.003 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " -0.086 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 201 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL N 63 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.022 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 6532 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6817 2.76 - 3.30: 37294 3.30 - 3.83: 74724 3.83 - 4.37: 91660 4.37 - 4.90: 148358 Nonbonded interactions: 358853 Sorted by model distance: nonbonded pdb=" O HOH G1105 " pdb=" O HOH G1317 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP K 57 " pdb=" OH TYR J 137 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN C 16 " pdb=" O HOH C 701 " model vdw 2.250 3.040 ... (remaining 358848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.980 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 38957 Z= 0.254 Angle : 0.791 16.804 52770 Z= 0.393 Chirality : 1.466 21.198 5827 Planarity : 0.006 0.117 6535 Dihedral : 16.385 139.986 14479 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.47 % Allowed : 15.08 % Favored : 83.45 % 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: -0.05 (0.11), residues: 4692 helix: 0.51 (0.09), residues: 2693 sheet: -0.44 (0.27), residues: 323 loop : -0.67 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 30 TYR 0.026 0.002 TYR M 435 PHE 0.038 0.002 PHE L 341 TRP 0.024 0.001 TRP N 53 HIS 0.012 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.00560 (38921) covalent geometry : angle 0.77080 (52677) hydrogen bonds : bond 0.06753 ( 1711) hydrogen bonds : angle 4.67230 ( 5133) metal coordination : bond 0.05316 ( 36) metal coordination : angle 4.31656 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 482 time to evaluate : 1.496 Fit side-chains REVERT: C 191 ASP cc_start: 0.8026 (m-30) cc_final: 0.6892 (t0) REVERT: C 389 LYS cc_start: 0.8881 (mppt) cc_final: 0.8533 (mmtm) REVERT: L 529 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7530 (mtt90) REVERT: M 56 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8156 (mm110) outliers start: 57 outliers final: 40 residues processed: 528 average time/residue: 0.8101 time to fit residues: 510.6370 Evaluate side-chains 506 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 466 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 295 LYS Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 196 ASN F 386 GLN F 400 HIS G 57 ASN G 88 GLN G 232 GLN G 583 ASN G 828 GLN ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN L 315 GLN M 45 GLN K 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.067745 restraints weight = 40271.312| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.09 r_work: 0.2811 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.253 38957 Z= 0.385 Angle : 2.469 50.832 52770 Z= 1.421 Chirality : 0.449 6.761 5827 Planarity : 0.004 0.061 6535 Dihedral : 11.091 140.513 6163 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.93 % Rotamer: Outliers : 2.30 % Allowed : 14.46 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4692 helix: 1.27 (0.10), residues: 2692 sheet: -0.23 (0.28), residues: 321 loop : -0.37 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.022 0.002 TYR M 435 PHE 0.029 0.001 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01106 (38921) covalent geometry : angle 2.15398 (52677) hydrogen bonds : bond 0.05605 ( 1711) hydrogen bonds : angle 4.19669 ( 5133) metal coordination : bond 0.06318 ( 36) metal coordination : angle 28.83455 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 490 time to evaluate : 1.592 Fit side-chains REVERT: F 243 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8534 (mmtm) REVERT: G 714 ARG cc_start: 0.8299 (ptm160) cc_final: 0.7658 (ttt-90) REVERT: I 27 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8479 (tptt) REVERT: L 570 ASN cc_start: 0.8193 (m-40) cc_final: 0.7814 (m110) REVERT: M 56 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7841 (mm110) REVERT: N 323 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7328 (ptt) outliers start: 89 outliers final: 42 residues processed: 539 average time/residue: 0.8597 time to fit residues: 551.7285 Evaluate side-chains 513 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 469 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 HIS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain J residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 121 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 368 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 357 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 345 optimal weight: 0.9980 chunk 373 optimal weight: 4.9990 chunk 379 optimal weight: 10.0000 chunk 442 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN E 98 HIS G 57 ASN G 88 GLN G 583 ASN G 768 ASN G 834 GLN ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 845 ASN C 135 ASN K 5 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.066988 restraints weight = 40212.661| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.08 r_work: 0.2788 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38957 Z= 0.395 Angle : 2.471 50.657 52770 Z= 1.423 Chirality : 0.445 6.625 5827 Planarity : 0.004 0.060 6535 Dihedral : 10.668 139.110 6136 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 14.54 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4692 helix: 1.53 (0.10), residues: 2698 sheet: -0.04 (0.28), residues: 319 loop : -0.25 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 427 TYR 0.020 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.032 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01137 (38921) covalent geometry : angle 2.15664 (52677) hydrogen bonds : bond 0.05751 ( 1711) hydrogen bonds : angle 4.16484 ( 5133) metal coordination : bond 0.04657 ( 36) metal coordination : angle 28.81532 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 490 time to evaluate : 1.509 Fit side-chains REVERT: G 714 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7676 (ttt-90) REVERT: H 31 PHE cc_start: 0.7734 (m-10) cc_final: 0.6755 (t80) REVERT: H 36 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: L 570 ASN cc_start: 0.8246 (m-40) cc_final: 0.7799 (m110) REVERT: M 48 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8773 (mp) REVERT: M 56 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7796 (mm110) REVERT: M 451 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7937 (mm-40) REVERT: N 323 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7328 (ptt) REVERT: K 46 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8033 (t80) REVERT: J 59 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7634 (t80) outliers start: 87 outliers final: 44 residues processed: 540 average time/residue: 0.8416 time to fit residues: 540.8818 Evaluate side-chains 519 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 469 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 449 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 chunk 417 optimal weight: 9.9990 chunk 419 optimal weight: 8.9990 chunk 404 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 383 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 57 ASN G 88 GLN G 218 ASN G 583 ASN G 655 HIS G 834 GLN G 839 GLN G 845 ASN H 208 HIS L 121 ASN L 212 ASN M 281 ASN N 7 ASN K 5 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.063725 restraints weight = 39030.279| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.06 r_work: 0.2713 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.253 38957 Z= 0.467 Angle : 2.495 50.606 52770 Z= 1.433 Chirality : 0.452 6.726 5827 Planarity : 0.005 0.057 6535 Dihedral : 11.379 138.772 6129 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Rotamer: Outliers : 2.79 % Allowed : 13.97 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.12), residues: 4692 helix: 1.28 (0.10), residues: 2704 sheet: -0.03 (0.28), residues: 318 loop : -0.22 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 813 TYR 0.023 0.002 TYR N 76 PHE 0.027 0.002 PHE L 341 TRP 0.026 0.002 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01270 (38921) covalent geometry : angle 2.18620 (52677) hydrogen bonds : bond 0.07678 ( 1711) hydrogen bonds : angle 4.53147 ( 5133) metal coordination : bond 0.06307 ( 36) metal coordination : angle 28.71866 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 465 time to evaluate : 1.375 Fit side-chains REVERT: G 87 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8742 (mtmp) REVERT: G 714 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7687 (ttt-90) REVERT: G 789 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: G 839 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: C 496 ASP cc_start: 0.8191 (t0) cc_final: 0.7849 (t0) REVERT: H 31 PHE cc_start: 0.7872 (m-10) cc_final: 0.6897 (t80) REVERT: H 36 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: L 570 ASN cc_start: 0.8406 (m-40) cc_final: 0.7953 (m110) REVERT: M 48 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8781 (mp) REVERT: M 56 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7745 (mm110) REVERT: M 265 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.6913 (mptt) REVERT: M 451 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: N 30 TRP cc_start: 0.8656 (t-100) cc_final: 0.7700 (t60) REVERT: N 485 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.2613 (mmp) REVERT: J 59 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7887 (t80) outliers start: 108 outliers final: 51 residues processed: 526 average time/residue: 0.8460 time to fit residues: 529.9937 Evaluate side-chains 522 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 462 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 839 GLN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 164 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 419 optimal weight: 2.9990 chunk 438 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 375 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN G 57 ASN G 88 GLN G 218 ASN G 583 ASN G 605 ASN G 845 ASN C 319 HIS ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS K 5 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067159 restraints weight = 39871.854| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.08 r_work: 0.2794 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38957 Z= 0.389 Angle : 2.473 50.677 52770 Z= 1.423 Chirality : 0.443 6.508 5827 Planarity : 0.004 0.054 6535 Dihedral : 10.768 138.925 6129 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 1.94 % Allowed : 15.00 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.28 (0.12), residues: 4692 helix: 1.64 (0.10), residues: 2694 sheet: 0.21 (0.29), residues: 299 loop : -0.25 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 813 TYR 0.023 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.029 0.001 TRP N 53 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01127 (38921) covalent geometry : angle 2.15573 (52677) hydrogen bonds : bond 0.05496 ( 1711) hydrogen bonds : angle 4.17532 ( 5133) metal coordination : bond 0.03713 ( 36) metal coordination : angle 28.95375 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 495 time to evaluate : 1.543 Fit side-chains REVERT: G 588 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8541 (ttpt) REVERT: G 714 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7743 (ttt-90) REVERT: G 902 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8306 (mp) REVERT: C 496 ASP cc_start: 0.8187 (t0) cc_final: 0.7857 (t0) REVERT: I 171 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8702 (mmtm) REVERT: H 31 PHE cc_start: 0.7783 (m-10) cc_final: 0.6800 (t80) REVERT: H 36 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: L 570 ASN cc_start: 0.8317 (m-40) cc_final: 0.7899 (m110) REVERT: M 48 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8725 (mp) REVERT: M 56 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7730 (mm110) REVERT: M 451 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: N 30 TRP cc_start: 0.8640 (t-100) cc_final: 0.7665 (t60) REVERT: K 46 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8011 (t80) REVERT: J 59 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7598 (t80) outliers start: 75 outliers final: 34 residues processed: 539 average time/residue: 0.8422 time to fit residues: 541.9740 Evaluate side-chains 515 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 474 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 390 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN B 76 HIS K 5 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.064905 restraints weight = 38818.296| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.08 r_work: 0.2734 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 38957 Z= 0.417 Angle : 2.480 50.634 52770 Z= 1.427 Chirality : 0.448 6.624 5827 Planarity : 0.004 0.057 6535 Dihedral : 10.923 137.859 6124 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 2.41 % Allowed : 14.64 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.23 (0.12), residues: 4692 helix: 1.56 (0.10), residues: 2700 sheet: 0.15 (0.29), residues: 311 loop : -0.19 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 529 TYR 0.021 0.002 TYR N 76 PHE 0.028 0.002 PHE J 3 TRP 0.034 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01174 (38921) covalent geometry : angle 2.16776 (52677) hydrogen bonds : bond 0.06585 ( 1711) hydrogen bonds : angle 4.31833 ( 5133) metal coordination : bond 0.05121 ( 36) metal coordination : angle 28.77761 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 465 time to evaluate : 1.700 Fit side-chains REVERT: F 252 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9041 (m-80) REVERT: G 588 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8545 (ttpt) REVERT: G 714 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7747 (ttt-90) REVERT: G 902 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 109 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8623 (mmt-90) REVERT: C 496 ASP cc_start: 0.8220 (t0) cc_final: 0.7878 (t0) REVERT: H 31 PHE cc_start: 0.7829 (m-10) cc_final: 0.6858 (t80) REVERT: H 36 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: L 570 ASN cc_start: 0.8367 (m-40) cc_final: 0.7936 (m110) REVERT: M 48 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8739 (mp) REVERT: M 56 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7778 (mm110) REVERT: M 165 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7614 (tppt) REVERT: M 451 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: N 30 TRP cc_start: 0.8641 (t-100) cc_final: 0.7667 (t60) REVERT: J 59 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7726 (t80) outliers start: 93 outliers final: 44 residues processed: 519 average time/residue: 0.8708 time to fit residues: 535.9913 Evaluate side-chains 515 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 462 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 413 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 433 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 379 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN G 845 ASN B 196 ASN K 5 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065873 restraints weight = 38561.936| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.04 r_work: 0.2759 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 38957 Z= 0.401 Angle : 2.476 50.647 52770 Z= 1.425 Chirality : 0.446 6.568 5827 Planarity : 0.004 0.056 6535 Dihedral : 10.815 137.210 6124 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 2.38 % Allowed : 14.72 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.30 (0.12), residues: 4692 helix: 1.63 (0.10), residues: 2694 sheet: 0.19 (0.29), residues: 310 loop : -0.16 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 427 TYR 0.019 0.002 TYR M 435 PHE 0.027 0.002 PHE L 341 TRP 0.037 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01146 (38921) covalent geometry : angle 2.16173 (52677) hydrogen bonds : bond 0.06130 ( 1711) hydrogen bonds : angle 4.26258 ( 5133) metal coordination : bond 0.04716 ( 36) metal coordination : angle 28.85224 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 474 time to evaluate : 1.642 Fit side-chains REVERT: G 588 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8534 (ttpt) REVERT: G 664 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8362 (mtm-85) REVERT: G 714 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7762 (ttt-90) REVERT: G 902 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 109 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8600 (mmt-90) REVERT: C 496 ASP cc_start: 0.8203 (t0) cc_final: 0.7866 (t0) REVERT: H 31 PHE cc_start: 0.7802 (m-10) cc_final: 0.6857 (t80) REVERT: H 36 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: L 570 ASN cc_start: 0.8347 (m-40) cc_final: 0.7906 (m110) REVERT: M 48 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8742 (mp) REVERT: M 56 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7768 (mm110) REVERT: M 165 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7587 (tppt) REVERT: M 451 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7799 (mm-40) REVERT: N 30 TRP cc_start: 0.8622 (t-100) cc_final: 0.7659 (t60) REVERT: N 485 MET cc_start: 0.2926 (OUTLIER) cc_final: 0.2572 (mmp) REVERT: K 46 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8050 (t80) REVERT: J 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7685 (t80) outliers start: 92 outliers final: 48 residues processed: 525 average time/residue: 0.8743 time to fit residues: 545.7510 Evaluate side-chains 528 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 469 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 88 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 328 optimal weight: 0.3980 chunk 361 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN K 5 GLN K 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.068088 restraints weight = 38895.101| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.05 r_work: 0.2810 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38957 Z= 0.383 Angle : 2.472 50.639 52770 Z= 1.422 Chirality : 0.442 6.486 5827 Planarity : 0.004 0.059 6535 Dihedral : 10.397 135.076 6124 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.13 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 15.24 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.12), residues: 4692 helix: 1.79 (0.10), residues: 2702 sheet: 0.32 (0.30), residues: 299 loop : -0.18 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 859 TYR 0.025 0.001 TYR M 435 PHE 0.031 0.001 PHE J 3 TRP 0.040 0.001 TRP N 53 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01118 (38921) covalent geometry : angle 2.15342 (52677) hydrogen bonds : bond 0.05171 ( 1711) hydrogen bonds : angle 4.07966 ( 5133) metal coordination : bond 0.03482 ( 36) metal coordination : angle 28.97911 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 486 time to evaluate : 1.644 Fit side-chains REVERT: G 588 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8511 (ttpt) REVERT: G 714 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7755 (ttt-90) REVERT: G 902 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8263 (mp) REVERT: C 109 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8599 (mmt-90) REVERT: H 31 PHE cc_start: 0.7735 (m-10) cc_final: 0.6805 (t80) REVERT: H 36 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: H 54 TRP cc_start: 0.8465 (t60) cc_final: 0.8099 (t-100) REVERT: L 570 ASN cc_start: 0.8293 (m-40) cc_final: 0.7847 (m110) REVERT: M 48 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8725 (mp) REVERT: M 56 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7769 (mm110) REVERT: M 165 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7574 (tppt) REVERT: M 451 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7791 (mm-40) REVERT: M 464 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: N 30 TRP cc_start: 0.8619 (t-100) cc_final: 0.7643 (t60) REVERT: N 53 TRP cc_start: 0.8508 (t-100) cc_final: 0.8144 (t60) REVERT: N 485 MET cc_start: 0.2845 (OUTLIER) cc_final: 0.2468 (mmp) REVERT: K 46 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8017 (t80) REVERT: J 59 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8402 (t80) outliers start: 74 outliers final: 38 residues processed: 531 average time/residue: 0.8730 time to fit residues: 549.8600 Evaluate side-chains 516 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 467 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 422 LEU Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 219 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN K 5 GLN K 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065883 restraints weight = 38749.475| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.08 r_work: 0.2757 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38957 Z= 0.403 Angle : 2.477 50.625 52770 Z= 1.425 Chirality : 0.446 6.580 5827 Planarity : 0.004 0.058 6535 Dihedral : 10.466 133.784 6116 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 1.81 % Allowed : 15.47 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.41 (0.12), residues: 4692 helix: 1.71 (0.10), residues: 2706 sheet: 0.23 (0.29), residues: 310 loop : -0.12 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 859 TYR 0.019 0.002 TYR M 207 PHE 0.026 0.002 PHE L 341 TRP 0.036 0.001 TRP N 53 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01149 (38921) covalent geometry : angle 2.16270 (52677) hydrogen bonds : bond 0.06122 ( 1711) hydrogen bonds : angle 4.21610 ( 5133) metal coordination : bond 0.04847 ( 36) metal coordination : angle 28.82404 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 466 time to evaluate : 1.620 Fit side-chains REVERT: G 588 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8523 (ttpt) REVERT: G 664 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8313 (mtm-85) REVERT: G 714 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7776 (ttt-90) REVERT: G 902 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 109 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8599 (mmt-90) REVERT: H 31 PHE cc_start: 0.7799 (m-10) cc_final: 0.6860 (t80) REVERT: H 36 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: L 570 ASN cc_start: 0.8329 (m-40) cc_final: 0.7821 (m110) REVERT: M 48 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8745 (mp) REVERT: M 56 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7777 (mm110) REVERT: M 165 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7609 (tppt) REVERT: M 451 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: N 30 TRP cc_start: 0.8629 (t-100) cc_final: 0.7677 (t60) REVERT: N 485 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.2474 (mmp) REVERT: J 59 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7575 (t80) outliers start: 70 outliers final: 39 residues processed: 509 average time/residue: 0.8809 time to fit residues: 532.5187 Evaluate side-chains 509 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 460 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 32 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 360 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 845 ASN K 5 GLN K 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066346 restraints weight = 38383.194| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.04 r_work: 0.2769 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.241 38957 Z= 0.398 Angle : 2.477 50.622 52770 Z= 1.425 Chirality : 0.445 6.555 5827 Planarity : 0.004 0.058 6535 Dihedral : 10.463 132.913 6116 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 1.50 % Allowed : 15.73 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.41 (0.12), residues: 4692 helix: 1.72 (0.10), residues: 2691 sheet: 0.22 (0.29), residues: 310 loop : -0.11 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 859 TYR 0.019 0.002 TYR M 435 PHE 0.030 0.001 PHE J 3 TRP 0.049 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01141 (38921) covalent geometry : angle 2.16172 (52677) hydrogen bonds : bond 0.05967 ( 1711) hydrogen bonds : angle 4.20812 ( 5133) metal coordination : bond 0.04515 ( 36) metal coordination : angle 28.86653 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 460 time to evaluate : 1.535 Fit side-chains REVERT: G 588 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8550 (ttpt) REVERT: G 664 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8297 (mtm-85) REVERT: G 714 ARG cc_start: 0.8226 (ptm160) cc_final: 0.7766 (ttt-90) REVERT: G 902 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 109 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (mmt-90) REVERT: H 31 PHE cc_start: 0.7797 (m-10) cc_final: 0.6857 (t80) REVERT: H 36 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: L 570 ASN cc_start: 0.8325 (m-40) cc_final: 0.7819 (m110) REVERT: M 48 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8738 (mp) REVERT: M 56 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7774 (mm110) REVERT: M 165 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7617 (tppt) REVERT: N 30 TRP cc_start: 0.8622 (t-100) cc_final: 0.7671 (t60) REVERT: N 53 TRP cc_start: 0.8532 (t-100) cc_final: 0.8176 (t60) REVERT: N 485 MET cc_start: 0.2899 (OUTLIER) cc_final: 0.2453 (mmp) REVERT: J 59 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7565 (t80) outliers start: 58 outliers final: 36 residues processed: 497 average time/residue: 0.8729 time to fit residues: 513.5934 Evaluate side-chains 503 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 458 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 588 LYS Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 168 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 392 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 375 optimal weight: 1.9990 chunk 394 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 466 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN K 5 GLN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.066269 restraints weight = 38616.262| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.05 r_work: 0.2767 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38957 Z= 0.398 Angle : 2.477 50.607 52770 Z= 1.425 Chirality : 0.445 6.557 5827 Planarity : 0.004 0.058 6535 Dihedral : 10.475 132.199 6116 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 1.63 % Allowed : 15.52 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.41 (0.12), residues: 4692 helix: 1.72 (0.10), residues: 2690 sheet: 0.22 (0.29), residues: 310 loop : -0.12 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 859 TYR 0.019 0.002 TYR M 435 PHE 0.027 0.002 PHE L 341 TRP 0.046 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01142 (38921) covalent geometry : angle 2.16213 (52677) hydrogen bonds : bond 0.06011 ( 1711) hydrogen bonds : angle 4.22199 ( 5133) metal coordination : bond 0.04532 ( 36) metal coordination : angle 28.86045 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26925.50 seconds wall clock time: 455 minutes 19.03 seconds (27319.03 seconds total)