Starting phenix.real_space_refine on Sat Mar 23 00:52:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oew_16838/03_2024/8oew_16838.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 1.056 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 Zn 8 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 212 5.16 5 C 21870 2.51 5 N 6151 2.21 5 O 6718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1389": "OD1" <-> "OD2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 743": "OD1" <-> "OD2" Residue "B TYR 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 138": "OD1" <-> "OD2" Residue "I ASP 29": "OD1" <-> "OD2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "M ASP 613": "OD1" <-> "OD2" Residue "M ASP 640": "OD1" <-> "OD2" Residue "M PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 643": "OE1" <-> "OE2" Residue "M ASP 661": "OD1" <-> "OD2" Residue "M PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 32": "OE1" <-> "OE2" Residue "Q GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11159 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1340} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1074 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "Q" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 69.733 99.369 57.029 1.00 55.63 S ATOM 494 SG CYS A 74 73.434 98.257 56.646 1.00 53.41 S ATOM 541 SG CYS A 81 71.478 97.206 59.783 1.00 43.12 S ATOM 776 SG CYS A 111 78.025 137.452 83.544 1.00 79.39 S ATOM 804 SG CYS A 114 80.442 138.586 81.099 1.00 78.95 S ATOM 1117 SG CYS A 154 80.950 139.353 84.771 1.00 89.81 S ATOM 1144 SG CYS A 184 78.172 141.243 82.685 1.00 87.15 S ATOM 19775 SG CYS B1196 85.699 108.766 59.849 1.00 51.07 S ATOM 19797 SG CYS B1199 83.417 109.517 62.765 1.00 50.76 S ATOM 19912 SG CYS B1214 82.034 108.961 59.277 1.00 61.29 S ATOM 19933 SG CYS B1217 83.998 112.208 60.245 1.00 68.34 S ATOM 20900 SG CYS C 88 67.316 31.592 67.669 1.00 42.39 S ATOM 20913 SG CYS C 90 64.872 34.431 66.712 1.00 53.45 S ATOM 20948 SG CYS C 94 63.905 30.874 67.660 1.00 33.19 S ATOM 20970 SG CYS C 97 65.105 33.368 70.347 1.00 29.03 S ATOM 28739 SG CYS I 86 58.841 88.610 157.312 1.00 59.16 S ATOM 28763 SG CYS I 89 55.644 86.922 158.659 1.00 61.10 S ATOM 28967 SG CYS I 114 56.521 86.683 154.962 1.00 49.30 S ATOM 29002 SG CYS I 119 55.382 89.971 156.639 1.00 53.99 S ATOM 28187 SG CYS I 17 48.086 128.522 141.160 1.00 81.19 S ATOM 28211 SG CYS I 20 47.209 128.566 137.366 1.00 82.04 S ATOM 28362 SG CYS I 39 50.584 129.681 138.381 1.00 89.78 S ATOM 28387 SG CYS I 42 47.714 131.808 139.329 1.00 94.48 S ATOM 29112 SG CYS J 7 65.198 41.314 100.489 1.00 10.76 S ATOM 29136 SG CYS J 10 67.097 38.064 99.769 1.00 14.19 S ATOM 29400 SG CYS J 44 67.751 40.228 103.012 1.00 15.14 S ATOM 29406 SG CYS J 45 64.866 37.916 102.520 1.00 16.53 S ATOM 30543 SG CYS L 19 31.661 61.763 81.008 1.00 54.09 S ATOM 30562 SG CYS L 22 29.206 58.982 80.646 1.00 61.21 S ATOM 30673 SG CYS L 36 28.996 61.716 78.238 1.00 63.51 S ATOM 30699 SG CYS L 39 28.149 62.525 81.949 1.00 64.33 S Time building chain proxies: 18.68, per 1000 atoms: 0.53 Number of scatterers: 35037 At special positions: 0 Unit cell: (157.5, 166.95, 200.55, 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) Zn 8 29.99 S 212 16.00 P 77 15.00 Mg 1 11.99 O 6718 8.00 N 6151 7.00 C 21870 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 - 3.50 Amino acid : False - 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: 13.60 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7876 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 47 sheets defined 39.4% alpha, 18.7% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 13.66 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.638A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.716A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.581A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.852A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.941A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.500A pdb=" N ASP A 691 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.546A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.585A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.811A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.933A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.502A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.509A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.502A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.911A pdb=" N LYS A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A1318 " --> pdb=" O ASP A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1318' Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.913A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.667A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.549A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.728A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.768A pdb=" N LYS B 438 " --> pdb=" O CYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.576A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.741A pdb=" N ILE B 787 " --> pdb=" O CYS B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.805A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1131 through 1135 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1242 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.699A pdb=" N ARG C 133 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.581A pdb=" N LYS D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 165 through 180 removed outlier: 4.008A pdb=" N LEU D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.730A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.516A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.310A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.604A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.686A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.566A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.550A pdb=" N GLN I 67 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.761A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 3.928A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.743A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.767A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 576 through 588 Processing helix chain 'M' and resid 589 through 592 Processing helix chain 'M' and resid 599 through 609 Proline residue: M 605 - end of helix Processing helix chain 'M' and resid 611 through 622 Processing helix chain 'M' and resid 625 through 641 removed outlier: 3.695A pdb=" N ASP M 630 " --> pdb=" O ILE M 626 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN M 631 " --> pdb=" O GLU M 627 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU M 632 " --> pdb=" O GLU M 628 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 634 " --> pdb=" O ASP M 630 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL M 635 " --> pdb=" O GLN M 631 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS M 636 " --> pdb=" O LEU M 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 639 " --> pdb=" O VAL M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 680 removed outlier: 3.566A pdb=" N PHE M 676 " --> pdb=" O LYS M 672 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS M 678 " --> pdb=" O ILE M 674 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 44 Processing helix chain 'O' and resid 54 through 58 removed outlier: 3.731A pdb=" N THR O 57 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 Processing helix chain 'O' and resid 98 through 110 removed outlier: 4.252A pdb=" N GLU O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.848A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.495A pdb=" N ARG B1227 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.469A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.300A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.654A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 7.798A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.572A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.125A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.474A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.225A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.723A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1244 through 1248 removed outlier: 4.206A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.317A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.431A pdb=" N TYR B 161 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE B 210 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 163 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 208 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 165 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 206 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 167 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA B 199 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 228 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 201 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 205 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN B 222 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN B 220 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 209 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.010A pdb=" N LYS M 688 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC5, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC6, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC7, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.771A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC9, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.513A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.323A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 904 through 906 removed outlier: 6.851A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 942 through 944 Processing sheet with id=AD8, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.291A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.411A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE3, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.536A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 86 removed outlier: 6.703A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.620A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.443A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 60 through 61 removed outlier: 3.781A pdb=" N THR Q 13 " --> pdb=" O GLU O 28 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA Q 73 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG Q 8 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL Q 75 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Q 78 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 19.22 Time building geometry restraints manager: 14.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10277 1.33 - 1.46: 6327 1.46 - 1.58: 18766 1.58 - 1.70: 150 1.70 - 1.82: 336 Bond restraints: 35856 Sorted by residual: bond pdb=" C ILE B1049 " pdb=" N PRO B1050 " ideal model delta sigma weight residual 1.335 1.385 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" CA VAL A 521 " pdb=" CB VAL A 521 " ideal model delta sigma weight residual 1.539 1.556 -0.017 5.40e-03 3.43e+04 9.38e+00 bond pdb=" N ARG Q 9 " pdb=" CA ARG Q 9 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.21e-02 6.83e+03 5.52e+00 bond pdb=" CB VAL B 886 " pdb=" CG2 VAL B 886 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" C3' DC T 33 " pdb=" O3' DC T 33 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.10e+00 ... (remaining 35851 not shown) Histogram of bond angle deviations from ideal: 97.10 - 105.01: 1001 105.01 - 112.92: 19242 112.92 - 120.83: 17165 120.83 - 128.74: 11101 128.74 - 136.64: 252 Bond angle restraints: 48761 Sorted by residual: angle pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta sigma weight residual 121.54 133.79 -12.25 1.91e+00 2.74e-01 4.12e+01 angle pdb=" C HIS Q 10 " pdb=" N LYS Q 11 " pdb=" CA LYS Q 11 " ideal model delta sigma weight residual 126.32 136.64 -10.32 1.74e+00 3.30e-01 3.52e+01 angle pdb=" C PHE O 52 " pdb=" N ALA O 53 " pdb=" CA ALA O 53 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 angle pdb=" N ARG Q 9 " pdb=" CA ARG Q 9 " pdb=" C ARG Q 9 " ideal model delta sigma weight residual 109.07 101.41 7.66 1.61e+00 3.86e-01 2.26e+01 angle pdb=" N GLN D 131 " pdb=" CA GLN D 131 " pdb=" CB GLN D 131 " ideal model delta sigma weight residual 110.39 118.15 -7.76 1.66e+00 3.63e-01 2.18e+01 ... (remaining 48756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 21169 35.10 - 70.21: 578 70.21 - 105.31: 36 105.31 - 140.41: 0 140.41 - 175.51: 1 Dihedral angle restraints: 21784 sinusoidal: 9616 harmonic: 12168 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 146.89 33.11 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA ASN D 144 " pdb=" C ASN D 144 " pdb=" N LEU D 145 " pdb=" CA LEU D 145 " ideal model delta harmonic sigma weight residual 180.00 147.68 32.32 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA ILE O 90 " pdb=" C ILE O 90 " pdb=" N PRO O 91 " pdb=" CA PRO O 91 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 21781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5132 0.103 - 0.206: 300 0.206 - 0.309: 11 0.309 - 0.412: 4 0.412 - 0.515: 1 Chirality restraints: 5448 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CG LEU A 831 " pdb=" CB LEU A 831 " pdb=" CD1 LEU A 831 " pdb=" CD2 LEU A 831 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CG LEU L 52 " pdb=" CB LEU L 52 " pdb=" CD1 LEU L 52 " pdb=" CD2 LEU L 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 5445 not shown) Planarity restraints: 6052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 539 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C GLN A 539 " -0.094 2.00e-02 2.50e+03 pdb=" O GLN A 539 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 540 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 829 " -0.028 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR B 829 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 829 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 829 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 829 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 829 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU M 604 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO M 605 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 605 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 605 " 0.039 5.00e-02 4.00e+02 ... (remaining 6049 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 495 2.65 - 3.21: 30318 3.21 - 3.77: 58262 3.77 - 4.34: 82304 4.34 - 4.90: 129763 Nonbonded interactions: 301142 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.087 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.136 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.152 2.170 nonbonded pdb=" O ASN D 76 " pdb=" OG1 THR D 110 " model vdw 2.210 2.440 ... (remaining 301137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 4.970 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: 0.040 Extract box with map and model: 20.150 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 111.250 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35856 Z= 0.305 Angle : 0.785 12.253 48761 Z= 0.435 Chirality : 0.052 0.515 5448 Planarity : 0.006 0.069 6052 Dihedral : 15.704 175.515 13908 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4128 helix: -0.48 (0.13), residues: 1462 sheet: -0.34 (0.20), residues: 603 loop : -0.75 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 479 HIS 0.011 0.001 HIS D 80 PHE 0.046 0.003 PHE A 431 TYR 0.059 0.002 TYR B 829 ARG 0.030 0.001 ARG A1153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 4.007 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.6793 (mtt) cc_final: 0.6583 (mtm) REVERT: I 93 GLU cc_start: 0.7971 (tt0) cc_final: 0.7716 (tt0) REVERT: K 1 MET cc_start: 0.7236 (ttm) cc_final: 0.6996 (ttm) REVERT: K 111 ASP cc_start: 0.7839 (m-30) cc_final: 0.7635 (m-30) REVERT: Q 46 LYS cc_start: 0.4745 (mmpt) cc_final: 0.4061 (pptt) REVERT: Q 52 ASP cc_start: 0.5728 (m-30) cc_final: 0.4631 (p0) REVERT: Q 65 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7580 (tm-30) REVERT: Q 79 PHE cc_start: 0.6080 (p90) cc_final: 0.4983 (m-80) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 1.6704 time to fit residues: 1171.9769 Evaluate side-chains 452 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN A 757 GLN A1384 HIS B 342 GLN B 538 GLN B 818 HIS B1084 ASN B1171 GLN C 51 GLN C 111 GLN C 217 GLN G 138 GLN H 76 ASN I 41 ASN I 45 GLN K 89 ASN M 578 HIS M 587 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35856 Z= 0.290 Angle : 0.610 13.384 48761 Z= 0.324 Chirality : 0.045 0.229 5448 Planarity : 0.005 0.050 6052 Dihedral : 12.619 172.850 5431 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.54 % Allowed : 9.80 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4128 helix: 0.38 (0.13), residues: 1483 sheet: -0.35 (0.21), residues: 574 loop : -0.61 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.010 0.001 HIS A1310 PHE 0.021 0.002 PHE Q 79 TYR 0.020 0.002 TYR O 79 ARG 0.008 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 470 time to evaluate : 4.185 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 317 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7809 (ttm) REVERT: A 735 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7525 (tp-100) REVERT: A 749 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7124 (tpt-90) REVERT: A 1262 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.4035 (mmm) REVERT: A 1279 MET cc_start: 0.4603 (ppp) cc_final: 0.4060 (tmm) REVERT: B 414 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7510 (mttp) REVERT: B 515 ARG cc_start: 0.7377 (tpp80) cc_final: 0.7150 (tpp80) REVERT: B 821 MET cc_start: 0.8957 (mtt) cc_final: 0.8676 (mtm) REVERT: I 93 GLU cc_start: 0.7968 (tt0) cc_final: 0.7709 (tt0) REVERT: K 1 MET cc_start: 0.7246 (ttm) cc_final: 0.6978 (ttm) REVERT: K 111 ASP cc_start: 0.7821 (m-30) cc_final: 0.7610 (m-30) REVERT: M 574 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4928 (ptm) REVERT: Q 65 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7671 (tm-30) REVERT: Q 79 PHE cc_start: 0.5799 (p90) cc_final: 0.5193 (m-10) outliers start: 57 outliers final: 23 residues processed: 492 average time/residue: 1.6498 time to fit residues: 957.6337 Evaluate side-chains 467 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 438 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 592 ILE Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 0.6980 chunk 256 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN A1303 GLN B 342 GLN B 727 ASN B 818 HIS B1084 ASN C 111 GLN E 133 GLN H 76 ASN I 45 GLN K 89 ASN ** M 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35856 Z= 0.236 Angle : 0.564 9.009 48761 Z= 0.298 Chirality : 0.044 0.191 5448 Planarity : 0.004 0.050 6052 Dihedral : 12.533 172.632 5431 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.73 % Allowed : 12.21 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4128 helix: 0.76 (0.14), residues: 1485 sheet: -0.32 (0.21), residues: 575 loop : -0.51 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 104 HIS 0.010 0.001 HIS A1310 PHE 0.024 0.002 PHE A 112 TYR 0.021 0.001 TYR O 79 ARG 0.006 0.000 ARG A1153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 453 time to evaluate : 4.408 Fit side-chains REVERT: A 290 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 317 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7818 (ttm) REVERT: A 447 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7947 (mt-10) REVERT: A 735 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7618 (tp-100) REVERT: A 749 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7078 (tpt-90) REVERT: B 821 MET cc_start: 0.8946 (mtt) cc_final: 0.8597 (mtm) REVERT: H 21 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8550 (mtpt) REVERT: H 70 LEU cc_start: 0.8491 (mm) cc_final: 0.8217 (mt) REVERT: I 93 GLU cc_start: 0.7953 (tt0) cc_final: 0.7699 (tt0) REVERT: K 111 ASP cc_start: 0.7820 (m-30) cc_final: 0.7606 (m-30) REVERT: M 593 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: Q 79 PHE cc_start: 0.5830 (p90) cc_final: 0.5019 (m-10) outliers start: 64 outliers final: 24 residues processed: 480 average time/residue: 1.5795 time to fit residues: 899.8001 Evaluate side-chains 460 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 431 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 593 PHE Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain Q residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 1.9990 chunk 197 optimal weight: 0.0770 chunk 359 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN A1303 GLN B 342 GLN B 727 ASN B 818 HIS B1084 ASN C 51 GLN C 111 GLN H 76 ASN I 45 GLN I 67 GLN K 89 ASN M 578 HIS M 587 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35856 Z= 0.229 Angle : 0.556 10.112 48761 Z= 0.292 Chirality : 0.043 0.202 5448 Planarity : 0.004 0.047 6052 Dihedral : 12.488 172.299 5431 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 13.50 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4128 helix: 0.99 (0.14), residues: 1490 sheet: -0.30 (0.20), residues: 593 loop : -0.47 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.009 0.001 HIS A1310 PHE 0.019 0.002 PHE Q 62 TYR 0.021 0.001 TYR O 79 ARG 0.008 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 463 time to evaluate : 4.092 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 317 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7804 (ttm) REVERT: A 330 GLN cc_start: 0.6346 (mm-40) cc_final: 0.6058 (mm-40) REVERT: A 447 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 735 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7836 (tp-100) REVERT: A 749 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7015 (tpt-90) REVERT: A 1262 MET cc_start: 0.4698 (OUTLIER) cc_final: 0.4300 (mpp) REVERT: B 414 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7551 (mttp) REVERT: B 726 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7968 (p0) REVERT: F 94 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7206 (mtm) REVERT: G 94 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8169 (mtmm) REVERT: K 17 LYS cc_start: 0.8267 (mtmt) cc_final: 0.8060 (mtpp) REVERT: K 111 ASP cc_start: 0.7832 (m-30) cc_final: 0.7608 (m-30) REVERT: M 593 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: O 82 ARG cc_start: 0.5481 (ptp-110) cc_final: 0.5279 (ptp-110) REVERT: Q 45 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.2634 (m-80) REVERT: Q 65 GLN cc_start: 0.8032 (tm130) cc_final: 0.7738 (tm130) REVERT: Q 79 PHE cc_start: 0.5878 (p90) cc_final: 0.4920 (m-10) outliers start: 72 outliers final: 31 residues processed: 495 average time/residue: 1.5934 time to fit residues: 936.1919 Evaluate side-chains 470 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 429 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 593 PHE Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain M residue 635 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 531 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN A1303 GLN B 222 GLN B 342 GLN B 818 HIS B 826 HIS B1084 ASN D 135 HIS H 76 ASN I 45 GLN K 89 ASN M 578 HIS M 587 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 35856 Z= 0.456 Angle : 0.651 12.179 48761 Z= 0.341 Chirality : 0.048 0.250 5448 Planarity : 0.005 0.050 6052 Dihedral : 12.628 170.286 5431 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.46 % Allowed : 14.72 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 4128 helix: 0.83 (0.14), residues: 1483 sheet: -0.34 (0.20), residues: 611 loop : -0.48 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.028 0.001 HIS M 578 PHE 0.024 0.002 PHE A 112 TYR 0.021 0.002 TYR B1125 ARG 0.009 0.001 ARG A1153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 438 time to evaluate : 4.401 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7868 (tm) REVERT: A 290 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 317 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: A 330 GLN cc_start: 0.6343 (mm-40) cc_final: 0.6003 (mm-40) REVERT: A 447 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8010 (mt-10) REVERT: A 735 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7910 (tp-100) REVERT: A 749 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7021 (tpt-90) REVERT: A 1288 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8172 (mm) REVERT: A 1412 MET cc_start: 0.8864 (ttp) cc_final: 0.8663 (ttp) REVERT: B 414 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7492 (mttp) REVERT: B 515 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6995 (tpp80) REVERT: B 726 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8208 (p0) REVERT: B 743 ASP cc_start: 0.7949 (p0) cc_final: 0.7719 (p0) REVERT: B 946 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8157 (ttmt) REVERT: B 1153 GLU cc_start: 0.7548 (tt0) cc_final: 0.7245 (tt0) REVERT: F 94 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7402 (mtm) REVERT: G 94 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: H 147 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8504 (mtpt) REVERT: K 111 ASP cc_start: 0.7866 (m-30) cc_final: 0.7635 (m-30) REVERT: M 574 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4994 (ptm) REVERT: Q 45 TYR cc_start: 0.4083 (OUTLIER) cc_final: 0.2824 (m-80) REVERT: Q 65 GLN cc_start: 0.8200 (tm130) cc_final: 0.7829 (tm130) outliers start: 91 outliers final: 39 residues processed: 489 average time/residue: 1.5777 time to fit residues: 915.5404 Evaluate side-chains 470 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 418 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 805 MET Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain M residue 635 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 TYR Chi-restraints excluded: chain Q residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 7.9990 chunk 361 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 401 optimal weight: 0.1980 chunk 333 optimal weight: 0.9990 chunk 185 optimal weight: 0.0020 chunk 33 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 531 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN A1303 GLN B 342 GLN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B1084 ASN C 217 GLN H 76 ASN I 45 GLN K 89 ASN M 578 HIS M 587 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35856 Z= 0.172 Angle : 0.538 11.936 48761 Z= 0.283 Chirality : 0.042 0.181 5448 Planarity : 0.004 0.051 6052 Dihedral : 12.496 173.343 5431 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.11 % Allowed : 15.59 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.13), residues: 4128 helix: 1.20 (0.14), residues: 1475 sheet: -0.15 (0.21), residues: 577 loop : -0.36 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1192 HIS 0.009 0.001 HIS A1310 PHE 0.028 0.001 PHE Q 62 TYR 0.013 0.001 TYR I 54 ARG 0.012 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 461 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7777 (tm) REVERT: A 317 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7842 (ttm) REVERT: A 447 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 735 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7873 (tp-100) REVERT: A 749 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7008 (tpt-90) REVERT: A 1101 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: B 414 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7495 (mttp) REVERT: B 424 MET cc_start: 0.7893 (ttm) cc_final: 0.7073 (ttm) REVERT: B 743 ASP cc_start: 0.7833 (p0) cc_final: 0.7486 (p0) REVERT: B 946 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8114 (ttmt) REVERT: B 1001 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8741 (ttm170) REVERT: B 1153 GLU cc_start: 0.7504 (tt0) cc_final: 0.7176 (tt0) REVERT: F 94 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7260 (mtm) REVERT: H 70 LEU cc_start: 0.8440 (mm) cc_final: 0.8196 (mt) REVERT: H 147 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8505 (mttt) REVERT: I 18 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: K 111 ASP cc_start: 0.7842 (m-30) cc_final: 0.7615 (m-30) REVERT: M 645 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.5754 (mmt180) REVERT: Q 36 LYS cc_start: 0.5924 (mppt) cc_final: 0.5355 (pptt) REVERT: Q 45 TYR cc_start: 0.4222 (OUTLIER) cc_final: 0.3120 (m-80) REVERT: Q 65 GLN cc_start: 0.8161 (tm130) cc_final: 0.7804 (tm130) outliers start: 78 outliers final: 25 residues processed: 502 average time/residue: 1.6710 time to fit residues: 991.4465 Evaluate side-chains 467 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 431 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 1001 ARG Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain M residue 691 PHE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 338 optimal weight: 0.0980 chunk 224 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 243 optimal weight: 0.1980 chunk 184 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 342 GLN B 818 HIS B1084 ASN C 217 GLN H 76 ASN I 45 GLN K 89 ASN M 578 HIS M 587 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35856 Z= 0.169 Angle : 0.537 11.396 48761 Z= 0.280 Chirality : 0.042 0.180 5448 Planarity : 0.004 0.054 6052 Dihedral : 12.435 172.923 5431 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4128 helix: 1.36 (0.14), residues: 1464 sheet: -0.10 (0.21), residues: 585 loop : -0.26 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1192 HIS 0.029 0.001 HIS M 578 PHE 0.028 0.001 PHE A 112 TYR 0.027 0.001 TYR O 76 ARG 0.012 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 451 time to evaluate : 3.843 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7908 (tm) REVERT: A 317 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: A 735 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7842 (tp-100) REVERT: A 749 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6971 (tpt-90) REVERT: A 1228 MET cc_start: 0.7812 (mtm) cc_final: 0.7595 (mtm) REVERT: A 1262 MET cc_start: 0.4793 (OUTLIER) cc_final: 0.3959 (mmm) REVERT: B 332 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7030 (ptt90) REVERT: B 743 ASP cc_start: 0.7836 (p0) cc_final: 0.7480 (p0) REVERT: B 946 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: B 1001 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8704 (ttm170) REVERT: B 1153 GLU cc_start: 0.7551 (tt0) cc_final: 0.7242 (tt0) REVERT: B 1240 MET cc_start: 0.8605 (mtp) cc_final: 0.8342 (mtt) REVERT: F 94 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7241 (mtp) REVERT: H 70 LEU cc_start: 0.8455 (mm) cc_final: 0.8201 (mt) REVERT: I 18 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: K 111 ASP cc_start: 0.7836 (m-30) cc_final: 0.7610 (m-30) REVERT: M 645 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5800 (mmt180) REVERT: Q 45 TYR cc_start: 0.4212 (OUTLIER) cc_final: 0.3090 (m-80) REVERT: Q 65 GLN cc_start: 0.8152 (tm130) cc_final: 0.7816 (tm130) outliers start: 56 outliers final: 22 residues processed: 486 average time/residue: 1.5984 time to fit residues: 925.0892 Evaluate side-chains 464 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 1001 ARG Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.0470 chunk 254 optimal weight: 0.7980 chunk 272 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 314 optimal weight: 0.7980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 342 GLN B 497 GLN B 818 HIS B 832 GLN B1084 ASN C 217 GLN H 76 ASN I 45 GLN K 89 ASN M 578 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35856 Z= 0.155 Angle : 0.534 11.463 48761 Z= 0.278 Chirality : 0.042 0.196 5448 Planarity : 0.004 0.058 6052 Dihedral : 12.360 173.063 5431 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.35 % Allowed : 17.37 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 4128 helix: 1.51 (0.14), residues: 1461 sheet: -0.02 (0.21), residues: 573 loop : -0.24 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.010 0.001 HIS M 578 PHE 0.033 0.001 PHE Q 62 TYR 0.026 0.001 TYR O 76 ARG 0.014 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 449 time to evaluate : 3.619 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7810 (tm) REVERT: A 317 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7827 (ttm) REVERT: A 735 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7782 (tp-100) REVERT: A 1228 MET cc_start: 0.7784 (mtm) cc_final: 0.7568 (mtm) REVERT: A 1262 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.3840 (mmm) REVERT: B 332 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7095 (ptt90) REVERT: B 1001 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8496 (ttp-110) REVERT: B 1153 GLU cc_start: 0.7500 (tt0) cc_final: 0.7199 (tt0) REVERT: B 1240 MET cc_start: 0.8592 (mtp) cc_final: 0.8372 (mtt) REVERT: F 100 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7016 (mtp-110) REVERT: H 70 LEU cc_start: 0.8472 (mm) cc_final: 0.8233 (mt) REVERT: I 18 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: I 58 ILE cc_start: 0.7693 (mm) cc_final: 0.7396 (mt) REVERT: K 111 ASP cc_start: 0.7820 (m-30) cc_final: 0.7598 (m-30) REVERT: Q 36 LYS cc_start: 0.6721 (mptt) cc_final: 0.6226 (pptt) REVERT: Q 45 TYR cc_start: 0.3878 (OUTLIER) cc_final: 0.2811 (m-80) REVERT: Q 65 GLN cc_start: 0.8091 (tm130) cc_final: 0.7774 (tm130) outliers start: 50 outliers final: 25 residues processed: 475 average time/residue: 1.5204 time to fit residues: 861.9008 Evaluate side-chains 453 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 421 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 1001 ARG Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.6980 chunk 383 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 292 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 336 optimal weight: 0.8980 chunk 352 optimal weight: 7.9990 chunk 371 optimal weight: 2.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 673 GLN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 818 HIS B 832 GLN B1084 ASN C 217 GLN E 129 GLN G 138 GLN H 76 ASN I 45 GLN I 67 GLN K 89 ASN M 578 HIS ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 35856 Z= 0.487 Angle : 0.679 12.070 48761 Z= 0.353 Chirality : 0.049 0.268 5448 Planarity : 0.005 0.061 6052 Dihedral : 12.583 169.781 5431 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.49 % Allowed : 17.70 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4128 helix: 0.98 (0.14), residues: 1482 sheet: -0.27 (0.20), residues: 617 loop : -0.33 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 104 HIS 0.021 0.002 HIS M 578 PHE 0.027 0.003 PHE B 479 TYR 0.033 0.002 TYR B 237 ARG 0.015 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 433 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7878 (ttm) REVERT: A 735 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7792 (tp-100) REVERT: A 749 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7048 (tpt-90) REVERT: A 1101 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: A 1153 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7256 (ttm110) REVERT: B 671 MET cc_start: 0.7635 (mtm) cc_final: 0.7414 (mtm) REVERT: B 946 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: B 1153 GLU cc_start: 0.7658 (tt0) cc_final: 0.7375 (tt0) REVERT: F 80 MET cc_start: 0.8588 (mmm) cc_final: 0.8369 (mmt) REVERT: F 100 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6983 (mtp-110) REVERT: I 18 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7684 (mp10) REVERT: I 58 ILE cc_start: 0.7751 (mm) cc_final: 0.7430 (mt) REVERT: I 93 GLU cc_start: 0.8063 (tt0) cc_final: 0.7843 (tt0) REVERT: K 111 ASP cc_start: 0.7866 (m-30) cc_final: 0.7631 (m-30) REVERT: L 27 GLU cc_start: 0.6308 (tp30) cc_final: 0.6048 (tp30) REVERT: Q 45 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.2988 (m-80) outliers start: 55 outliers final: 29 residues processed: 466 average time/residue: 1.6406 time to fit residues: 910.4970 Evaluate side-chains 452 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 416 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 805 MET Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 0.5980 chunk 394 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 186 optimal weight: 0.0770 chunk 274 optimal weight: 0.8980 chunk 413 optimal weight: 0.0060 chunk 380 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 254 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 673 GLN A 723 ASN A 757 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 497 GLN B 818 HIS B1084 ASN C 217 GLN H 76 ASN I 45 GLN K 89 ASN M 578 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35856 Z= 0.172 Angle : 0.563 11.577 48761 Z= 0.293 Chirality : 0.043 0.206 5448 Planarity : 0.004 0.063 6052 Dihedral : 12.462 173.446 5431 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.08 % Allowed : 18.24 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4128 helix: 1.30 (0.14), residues: 1471 sheet: -0.11 (0.21), residues: 589 loop : -0.27 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1192 HIS 0.009 0.001 HIS M 578 PHE 0.031 0.001 PHE Q 62 TYR 0.018 0.001 TYR I 54 ARG 0.016 0.000 ARG B 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 437 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7789 (ttm) REVERT: A 735 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7745 (tp-100) REVERT: A 749 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7074 (tpt-90) REVERT: A 1153 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7313 (ttm110) REVERT: A 1262 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.3831 (mtp) REVERT: B 332 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7006 (ptt90) REVERT: B 946 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: B 1153 GLU cc_start: 0.7604 (tt0) cc_final: 0.7322 (tt0) REVERT: F 100 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: F 121 ASP cc_start: 0.7934 (p0) cc_final: 0.7346 (p0) REVERT: H 70 LEU cc_start: 0.8408 (mm) cc_final: 0.8175 (mt) REVERT: I 18 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: K 111 ASP cc_start: 0.7837 (m-30) cc_final: 0.7598 (m-30) REVERT: L 27 GLU cc_start: 0.6179 (tp30) cc_final: 0.5926 (tp30) REVERT: M 573 LYS cc_start: 0.5901 (mmtt) cc_final: 0.5450 (tmtt) REVERT: M 645 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5938 (mmt180) REVERT: O 82 ARG cc_start: 0.5874 (ptp-110) cc_final: 0.5424 (tpt170) REVERT: Q 36 LYS cc_start: 0.6598 (mptt) cc_final: 0.6150 (pptt) REVERT: Q 45 TYR cc_start: 0.3916 (OUTLIER) cc_final: 0.3071 (m-80) REVERT: Q 65 GLN cc_start: 0.8166 (tm130) cc_final: 0.7823 (tm130) outliers start: 40 outliers final: 23 residues processed: 462 average time/residue: 1.5930 time to fit residues: 876.5265 Evaluate side-chains 458 residues out of total 3704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 427 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 5.9990 chunk 350 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 329 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN A 757 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 497 GLN B1084 ASN C 217 GLN E 129 GLN H 76 ASN I 45 GLN I 67 GLN K 89 ASN ** M 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114599 restraints weight = 50238.883| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.81 r_work: 0.3083 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35856 Z= 0.227 Angle : 0.574 11.996 48761 Z= 0.297 Chirality : 0.043 0.200 5448 Planarity : 0.004 0.065 6052 Dihedral : 12.441 172.242 5431 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.30 % Allowed : 18.35 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4128 helix: 1.31 (0.14), residues: 1478 sheet: -0.12 (0.21), residues: 594 loop : -0.27 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1192 HIS 0.008 0.001 HIS M 578 PHE 0.025 0.002 PHE Q 15 TYR 0.021 0.001 TYR B 237 ARG 0.015 0.000 ARG B 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14968.72 seconds wall clock time: 264 minutes 47.77 seconds (15887.77 seconds total)