Starting phenix.real_space_refine (version: dev) on Thu Dec 22 21:46:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/12_2022/7adc_11723_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.016 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 106": "OE1" <-> "OE2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f GLU 329": "OE1" <-> "OE2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 125": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a GLU 329": "OE1" <-> "OE2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b GLU 329": "OE1" <-> "OE2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 106": "OE1" <-> "OE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c GLU 329": "OE1" <-> "OE2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "d ARG 28": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d GLU 106": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "e ARG 28": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e GLU 106": "OE1" <-> "OE2" Residue "e GLU 108": "OE1" <-> "OE2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U GLU 122": "OE1" <-> "OE2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "U GLU 229": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "V GLU 181": "OE1" <-> "OE2" Residue "V GLU 188": "OE1" <-> "OE2" Residue "V GLU 204": "OE1" <-> "OE2" Residue "V ARG 265": "NH1" <-> "NH2" Residue "W GLU 71": "OE1" <-> "OE2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X ARG 268": "NH1" <-> "NH2" Residue "X ARG 371": "NH1" <-> "NH2" Residue "X GLU 379": "OE1" <-> "OE2" Residue "X ARG 451": "NH1" <-> "NH2" Residue "X GLU 477": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 565": "OE1" <-> "OE2" Residue "X ARG 647": "NH1" <-> "NH2" Residue "X GLU 867": "OE1" <-> "OE2" Residue "X GLU 876": "OE1" <-> "OE2" Residue "X GLU 898": "OE1" <-> "OE2" Residue "X ARG 903": "NH1" <-> "NH2" Residue "X GLU 963": "OE1" <-> "OE2" Residue "X ARG 996": "NH1" <-> "NH2" Residue "X ARG 1034": "NH1" <-> "NH2" Residue "X ARG 1106": "NH1" <-> "NH2" Residue "X ARG 1171": "NH1" <-> "NH2" Residue "X GLU 1174": "OE1" <-> "OE2" Residue "X GLU 1279": "OE1" <-> "OE2" Residue "X GLU 1321": "OE1" <-> "OE2" Residue "X GLU 1329": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y ARG 101": "NH1" <-> "NH2" Residue "Y ARG 133": "NH1" <-> "NH2" Residue "Y GLU 183": "OE1" <-> "OE2" Residue "Y GLU 195": "OE1" <-> "OE2" Residue "Y ARG 250": "NH1" <-> "NH2" Residue "Y GLU 301": "OE1" <-> "OE2" Residue "Y ARG 314": "NH1" <-> "NH2" Residue "Y GLU 402": "OE1" <-> "OE2" Residue "Y GLU 414": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y GLU 443": "OE1" <-> "OE2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ARG 515": "NH1" <-> "NH2" Residue "Y ARG 634": "NH1" <-> "NH2" Residue "Y GLU 677": "OE1" <-> "OE2" Residue "Y ARG 692": "NH1" <-> "NH2" Residue "Y GLU 714": "OE1" <-> "OE2" Residue "Y ARG 836": "NH1" <-> "NH2" Residue "Y GLU 866": "OE1" <-> "OE2" Residue "Y GLU 874": "OE1" <-> "OE2" Residue "Y ARG 933": "NH1" <-> "NH2" Residue "Y ARG 943": "NH1" <-> "NH2" Residue "Y ARG 1036": "NH1" <-> "NH2" Residue "Y ARG 1148": "NH1" <-> "NH2" Residue "Y GLU 1187": "OE1" <-> "OE2" Residue "Y GLU 1188": "OE1" <-> "OE2" Residue "Y GLU 1215": "OE1" <-> "OE2" Residue "Y ARG 1258": "NH1" <-> "NH2" Residue "Y GLU 1327": "OE1" <-> "OE2" Residue "Y ARG 1345": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51565 Number of models: 1 Model: "" Number of chains: 26 Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} Chain: "W" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 682 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 20} Chain breaks: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" 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: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 55.781 119.368 118.676 1.00132.17 S ATOM 39518 SG CYS Y 72 55.851 116.963 121.610 1.00141.56 S ATOM 39650 SG CYS Y 88 56.884 119.450 123.963 1.00131.23 S ATOM 45338 SG CYS Y 814 70.313 185.472 120.093 1.00 77.05 S ATOM 45903 SG CYS Y 888 71.680 181.458 120.146 1.00 71.20 S ATOM 45954 SG CYS Y 895 70.584 182.742 116.905 1.00 70.90 S ATOM 45975 SG CYS Y 898 73.251 184.751 118.230 1.00 63.61 S Time building chain proxies: 27.60, per 1000 atoms: 0.54 Number of scatterers: 51565 At special positions: 0 Unit cell: (161.2, 226.92, 194.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 96 15.00 Mg 6 11.99 F 15 9.00 O 10104 8.00 N 9111 7.00 C 32003 6.00 Be 5 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.96 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " Number of angles added : 6 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 221 helices and 48 sheets defined 35.6% alpha, 11.0% beta 30 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 18.79 Creating SS restraints... Processing helix chain 'f' and resid 3 through 7 Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 31 through 45 removed outlier: 3.809A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 124 through 128 Processing helix chain 'f' and resid 156 through 165 removed outlier: 4.376A pdb=" N VAL f 161 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 198 Processing helix chain 'f' and resid 213 through 220 Processing helix chain 'f' and resid 236 through 255 Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 292 through 302 removed outlier: 3.854A pdb=" N ARG f 296 " --> pdb=" O ALA f 293 " (cutoff:3.500A) Proline residue: f 297 - end of helix Processing helix chain 'f' and resid 326 through 334 Processing helix chain 'f' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 374 through 389 Proline residue: f 389 - end of helix Processing helix chain 'f' and resid 393 through 405 Processing helix chain 'f' and resid 409 through 415 Processing helix chain 'a' and resid 3 through 7 Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 31 through 45 removed outlier: 3.808A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 89 Processing helix chain 'a' and resid 124 through 128 Processing helix chain 'a' and resid 156 through 165 removed outlier: 4.377A pdb=" N VAL a 161 " --> pdb=" O THR a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 198 Processing helix chain 'a' and resid 213 through 220 Processing helix chain 'a' and resid 236 through 255 Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 292 through 302 removed outlier: 3.855A pdb=" N ARG a 296 " --> pdb=" O ALA a 293 " (cutoff:3.500A) Proline residue: a 297 - end of helix Processing helix chain 'a' and resid 326 through 334 Processing helix chain 'a' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 374 through 389 Proline residue: a 389 - end of helix Processing helix chain 'a' and resid 393 through 405 Processing helix chain 'a' and resid 409 through 415 Processing helix chain 'b' and resid 3 through 7 Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 31 through 45 removed outlier: 3.809A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 124 through 128 Processing helix chain 'b' and resid 156 through 165 removed outlier: 4.376A pdb=" N VAL b 161 " --> pdb=" O THR b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 198 Processing helix chain 'b' and resid 213 through 220 Processing helix chain 'b' and resid 236 through 255 Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 292 through 302 removed outlier: 3.855A pdb=" N ARG b 296 " --> pdb=" O ALA b 293 " (cutoff:3.500A) Proline residue: b 297 - end of helix Processing helix chain 'b' and resid 326 through 334 Processing helix chain 'b' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 374 through 389 Proline residue: b 389 - end of helix Processing helix chain 'b' and resid 393 through 405 Processing helix chain 'b' and resid 409 through 415 Processing helix chain 'c' and resid 3 through 7 Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 31 through 45 removed outlier: 3.809A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 89 Processing helix chain 'c' and resid 124 through 128 Processing helix chain 'c' and resid 156 through 165 removed outlier: 4.375A pdb=" N VAL c 161 " --> pdb=" O THR c 158 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 198 Processing helix chain 'c' and resid 213 through 220 Processing helix chain 'c' and resid 236 through 255 Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 292 through 302 removed outlier: 3.855A pdb=" N ARG c 296 " --> pdb=" O ALA c 293 " (cutoff:3.500A) Proline residue: c 297 - end of helix Processing helix chain 'c' and resid 326 through 334 Processing helix chain 'c' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 374 through 389 Proline residue: c 389 - end of helix Processing helix chain 'c' and resid 393 through 405 Processing helix chain 'c' and resid 409 through 415 Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 31 through 45 removed outlier: 3.809A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 89 Processing helix chain 'd' and resid 124 through 128 Processing helix chain 'd' and resid 156 through 165 removed outlier: 4.377A pdb=" N VAL d 161 " --> pdb=" O THR d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 198 Processing helix chain 'd' and resid 213 through 220 Processing helix chain 'd' and resid 236 through 255 Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 292 through 302 removed outlier: 3.854A pdb=" N ARG d 296 " --> pdb=" O ALA d 293 " (cutoff:3.500A) Proline residue: d 297 - end of helix Processing helix chain 'd' and resid 326 through 334 Processing helix chain 'd' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 374 through 389 Proline residue: d 389 - end of helix Processing helix chain 'd' and resid 393 through 405 Processing helix chain 'd' and resid 409 through 415 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 31 through 45 removed outlier: 3.809A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 89 Processing helix chain 'e' and resid 124 through 128 Processing helix chain 'e' and resid 156 through 165 removed outlier: 4.376A pdb=" N VAL e 161 " --> pdb=" O THR e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 198 Processing helix chain 'e' and resid 213 through 220 Processing helix chain 'e' and resid 236 through 255 Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 292 through 302 removed outlier: 3.855A pdb=" N ARG e 296 " --> pdb=" O ALA e 293 " (cutoff:3.500A) Proline residue: e 297 - end of helix Processing helix chain 'e' and resid 326 through 334 Processing helix chain 'e' and resid 347 through 352 removed outlier: 3.654A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 374 through 389 Proline residue: e 389 - end of helix Processing helix chain 'e' and resid 393 through 405 Processing helix chain 'e' and resid 409 through 415 Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 104 through 133 removed outlier: 3.973A pdb=" N PHE A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N HIS A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 320 through 329 removed outlier: 6.048A pdb=" N ASN A 324 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU A 327 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 400 through 425 Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'U' and resid 35 through 49 Processing helix chain 'U' and resid 78 through 87 Processing helix chain 'U' and resid 112 through 114 No H-bonds generated for 'chain 'U' and resid 112 through 114' Processing helix chain 'U' and resid 213 through 232 Processing helix chain 'V' and resid 19 through 21 No H-bonds generated for 'chain 'V' and resid 19 through 21' Processing helix chain 'V' and resid 35 through 48 Processing helix chain 'V' and resid 78 through 86 Processing helix chain 'V' and resid 112 through 114 No H-bonds generated for 'chain 'V' and resid 112 through 114' Processing helix chain 'V' and resid 155 through 164 Processing helix chain 'V' and resid 213 through 231 removed outlier: 4.712A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE V 231 " --> pdb=" O GLN V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 254 No H-bonds generated for 'chain 'V' and resid 251 through 254' Processing helix chain 'V' and resid 257 through 259 No H-bonds generated for 'chain 'V' and resid 257 through 259' Processing helix chain 'V' and resid 264 through 272 Processing helix chain 'V' and resid 279 through 282 No H-bonds generated for 'chain 'V' and resid 279 through 282' Processing helix chain 'V' and resid 286 through 288 No H-bonds generated for 'chain 'V' and resid 286 through 288' Processing helix chain 'V' and resid 298 through 308 removed outlier: 3.519A pdb=" N ALA V 308 " --> pdb=" O LYS V 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 12 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 46 through 55 Processing helix chain 'W' and resid 61 through 79 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 29 through 38 Processing helix chain 'X' and resid 50 through 56 Processing helix chain 'X' and resid 82 through 88 Processing helix chain 'X' and resid 206 through 213 removed outlier: 4.268A pdb=" N LEU X 213 " --> pdb=" O ILE X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 224 Processing helix chain 'X' and resid 271 through 279 Processing helix chain 'X' and resid 289 through 294 removed outlier: 3.925A pdb=" N ALA X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY X 294 " --> pdb=" O GLU X 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 289 through 294' Processing helix chain 'X' and resid 319 through 328 Processing helix chain 'X' and resid 347 through 352 Processing helix chain 'X' and resid 359 through 370 Processing helix chain 'X' and resid 378 through 389 removed outlier: 3.657A pdb=" N SER X 383 " --> pdb=" O GLU X 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU X 384 " --> pdb=" O ALA X 380 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE X 385 " --> pdb=" O ALA X 381 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 399 through 408 Processing helix chain 'X' and resid 422 through 437 Processing helix chain 'X' and resid 456 through 478 removed outlier: 3.725A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 496 through 507 Processing helix chain 'X' and resid 520 through 527 Processing helix chain 'X' and resid 540 through 542 No H-bonds generated for 'chain 'X' and resid 540 through 542' Processing helix chain 'X' and resid 545 through 548 No H-bonds generated for 'chain 'X' and resid 545 through 548' Processing helix chain 'X' and resid 552 through 554 No H-bonds generated for 'chain 'X' and resid 552 through 554' Processing helix chain 'X' and resid 609 through 611 No H-bonds generated for 'chain 'X' and resid 609 through 611' Processing helix chain 'X' and resid 663 through 666 No H-bonds generated for 'chain 'X' and resid 663 through 666' Processing helix chain 'X' and resid 671 through 673 No H-bonds generated for 'chain 'X' and resid 671 through 673' Processing helix chain 'X' and resid 676 through 688 removed outlier: 3.746A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN X 688 " --> pdb=" O ASN X 684 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 711 removed outlier: 3.759A pdb=" N VAL X 708 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA X 709 " --> pdb=" O ARG X 706 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP X 711 " --> pdb=" O VAL X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 824 Processing helix chain 'X' and resid 897 through 905 Processing helix chain 'X' and resid 943 through 980 removed outlier: 3.523A pdb=" N VAL X 980 " --> pdb=" O ARG X 976 " (cutoff:3.500A) Processing helix chain 'X' and resid 983 through 989 Processing helix chain 'X' and resid 993 through 995 No H-bonds generated for 'chain 'X' and resid 993 through 995' Processing helix chain 'X' and resid 1004 through 1037 removed outlier: 5.201A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1100 through 1102 No H-bonds generated for 'chain 'X' and resid 1100 through 1102' Processing helix chain 'X' and resid 1110 through 1133 Processing helix chain 'X' and resid 1138 through 1149 Processing helix chain 'X' and resid 1168 through 1176 Processing helix chain 'X' and resid 1192 through 1201 Processing helix chain 'X' and resid 1239 through 1241 No H-bonds generated for 'chain 'X' and resid 1239 through 1241' Processing helix chain 'X' and resid 1272 through 1280 Processing helix chain 'X' and resid 1284 through 1291 Processing helix chain 'X' and resid 1300 through 1309 Processing helix chain 'X' and resid 1321 through 1332 Processing helix chain 'Y' and resid 27 through 33 Processing helix chain 'Y' and resid 95 through 99 Processing helix chain 'Y' and resid 114 through 117 No H-bonds generated for 'chain 'Y' and resid 114 through 117' Processing helix chain 'Y' and resid 123 through 127 Processing helix chain 'Y' and resid 132 through 139 Processing helix chain 'Y' and resid 162 through 169 removed outlier: 3.789A pdb=" N ALA Y 168 " --> pdb=" O GLN Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 182 through 190 Processing helix chain 'Y' and resid 195 through 207 Processing helix chain 'Y' and resid 212 through 229 Processing helix chain 'Y' and resid 234 through 237 Processing helix chain 'Y' and resid 264 through 284 Processing helix chain 'Y' and resid 289 through 307 Processing helix chain 'Y' and resid 333 through 335 No H-bonds generated for 'chain 'Y' and resid 333 through 335' Processing helix chain 'Y' and resid 337 through 340 No H-bonds generated for 'chain 'Y' and resid 337 through 340' Processing helix chain 'Y' and resid 370 through 376 Processing helix chain 'Y' and resid 378 through 387 Processing helix chain 'Y' and resid 394 through 403 Processing helix chain 'Y' and resid 409 through 415 Processing helix chain 'Y' and resid 431 through 433 No H-bonds generated for 'chain 'Y' and resid 431 through 433' Processing helix chain 'Y' and resid 451 through 457 removed outlier: 4.176A pdb=" N ALA Y 455 " --> pdb=" O PRO Y 451 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA Y 456 " --> pdb=" O LEU Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 474 through 482 Processing helix chain 'Y' and resid 504 through 514 Processing helix chain 'Y' and resid 530 through 538 Processing helix chain 'Y' and resid 574 through 581 removed outlier: 4.055A pdb=" N MET Y 581 " --> pdb=" O ALA Y 577 " (cutoff:3.500A) Processing helix chain 'Y' and resid 598 through 612 Processing helix chain 'Y' and resid 615 through 635 removed outlier: 4.339A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 650 through 669 Processing helix chain 'Y' and resid 675 through 702 Processing helix chain 'Y' and resid 721 through 727 Processing helix chain 'Y' and resid 734 through 741 Processing helix chain 'Y' and resid 769 through 803 removed outlier: 3.861A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 836 through 839 No H-bonds generated for 'chain 'Y' and resid 836 through 839' Processing helix chain 'Y' and resid 866 through 874 Processing helix chain 'Y' and resid 896 through 899 No H-bonds generated for 'chain 'Y' and resid 896 through 899' Processing helix chain 'Y' and resid 915 through 929 Proline residue: Y 926 - end of helix removed outlier: 4.656A pdb=" N GLN Y 929 " --> pdb=" O GLU Y 925 " (cutoff:3.500A) Processing helix chain 'Y' and resid 945 through 948 Processing helix chain 'Y' and resid 1138 through 1145 Processing helix chain 'Y' and resid 1217 through 1224 Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.534A pdb=" N THR Y1230 " --> pdb=" O VAL Y1226 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1250 through 1260 Processing helix chain 'Y' and resid 1282 through 1294 Processing helix chain 'Y' and resid 1309 through 1312 No H-bonds generated for 'chain 'Y' and resid 1309 through 1312' Processing helix chain 'Y' and resid 1319 through 1324 Processing helix chain 'Y' and resid 1328 through 1337 Processing helix chain 'Y' and resid 1348 through 1353 Processing helix chain 'Y' and resid 1362 through 1372 removed outlier: 3.580A pdb=" N ARG Y1372 " --> pdb=" O ASP Y1368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'f' and resid 79 through 81 removed outlier: 6.230A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 341 through 344 removed outlier: 7.932A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP f 265 " --> pdb=" O MET f 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU f 207 " --> pdb=" O ASP f 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 79 through 81 removed outlier: 6.230A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a' and resid 341 through 344 removed outlier: 7.933A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP a 265 " --> pdb=" O MET a 205 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU a 207 " --> pdb=" O ASP a 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 79 through 81 removed outlier: 6.230A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 341 through 344 removed outlier: 7.933A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP b 265 " --> pdb=" O MET b 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU b 207 " --> pdb=" O ASP b 265 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 79 through 81 removed outlier: 6.230A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 341 through 344 removed outlier: 7.933A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP c 265 " --> pdb=" O MET c 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU c 207 " --> pdb=" O ASP c 265 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'd' and resid 79 through 81 removed outlier: 6.230A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 341 through 344 removed outlier: 7.932A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ASP d 265 " --> pdb=" O MET d 205 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU d 207 " --> pdb=" O ASP d 265 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'e' and resid 79 through 81 removed outlier: 6.229A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'e' and resid 341 through 344 removed outlier: 7.932A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP e 265 " --> pdb=" O MET e 205 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU e 207 " --> pdb=" O ASP e 265 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 159 through 163 removed outlier: 5.442A pdb=" N ASP A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL A 142 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.519A pdb=" N LYS A 239 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 223 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 297 through 299 removed outlier: 6.160A pdb=" N GLU A 335 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 182 through 186 removed outlier: 7.191A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 24 through 28 Processing sheet with id= R, first strand: chain 'U' and resid 170 through 172 removed outlier: 6.763A pdb=" N LYS U 145 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL U 59 " --> pdb=" O ARG U 143 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG U 143 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE U 61 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N SER U 141 " --> pdb=" O ILE U 61 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'U' and resid 90 through 92 Processing sheet with id= T, first strand: chain 'U' and resid 108 through 111 Processing sheet with id= U, first strand: chain 'V' and resid 23 through 28 Processing sheet with id= V, first strand: chain 'V' and resid 90 through 92 Processing sheet with id= W, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.175A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 93 through 95 Processing sheet with id= Y, first strand: chain 'X' and resid 118 through 123 removed outlier: 3.746A pdb=" N SER X 72 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG X 101 " --> pdb=" O TYR X 70 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR X 70 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL X 103 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU X 68 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'X' and resid 143 through 145 Processing sheet with id= AA, first strand: chain 'X' and resid 148 through 151 Processing sheet with id= AB, first strand: chain 'X' and resid 154 through 160 removed outlier: 6.257A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 228 through 231 Processing sheet with id= AD, first strand: chain 'X' and resid 603 through 606 Processing sheet with id= AE, first strand: chain 'X' and resid 634 through 637 Processing sheet with id= AF, first strand: chain 'X' and resid 748 through 752 removed outlier: 5.708A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 1227 through 1232 removed outlier: 6.460A pdb=" N ILE X1096 " --> pdb=" O ALA X 803 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 830 through 839 removed outlier: 3.816A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 1065 through 1067 Processing sheet with id= AJ, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.241A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AL, first strand: chain 'Y' and resid 145 through 147 removed outlier: 4.071A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Y' and resid 350 through 354 Processing sheet with id= AN, first strand: chain 'Y' and resid 355 through 358 removed outlier: 5.939A pdb=" N ILE Y 447 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY Y 358 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU Y 449 " --> pdb=" O GLY Y 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'Y' and resid 547 through 557 Processing sheet with id= AP, first strand: chain 'Y' and resid 819 through 823 Processing sheet with id= AQ, first strand: chain 'Y' and resid 957 through 961 removed outlier: 4.166A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id= AS, first strand: chain 'Y' and resid 1046 through 1049 removed outlier: 3.834A pdb=" N GLN Y1049 " --> pdb=" O SER Y1058 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER Y1058 " --> pdb=" O GLN Y1049 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Y' and resid 1077 through 1079 Processing sheet with id= AU, first strand: chain 'Y' and resid 1162 through 1164 removed outlier: 3.617A pdb=" N LEU Y1175 " --> pdb=" O GLU Y1188 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Y' and resid 1264 through 1266 1687 hydrogen bonds defined for protein. 4707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 23.12 Time building geometry restraints manager: 23.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17069 1.34 - 1.46: 6841 1.46 - 1.58: 27981 1.58 - 1.70: 182 1.70 - 1.81: 409 Bond restraints: 52482 Sorted by residual: bond pdb=" C4' U R 24 " pdb=" O4' U R 24 " ideal model delta sigma weight residual 1.454 1.814 -0.360 1.50e-02 4.44e+03 5.78e+02 bond pdb=" BE BEF b1002 " pdb=" F2 BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF a1002 " pdb=" F2 BEF a1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF e1002 " pdb=" F2 BEF e1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" BE BEF c 504 " pdb=" F2 BEF c 504 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 52477 not shown) Histogram of bond angle deviations from ideal: 92.05 - 100.86: 104 100.86 - 109.68: 5850 109.68 - 118.49: 36502 118.49 - 127.31: 28240 127.31 - 136.12: 522 Bond angle restraints: 71218 Sorted by residual: angle pdb=" C4' U R 24 " pdb=" O4' U R 24 " pdb=" C1' U R 24 " ideal model delta sigma weight residual 109.70 92.05 17.65 1.00e+00 1.00e+00 3.11e+02 angle pdb=" C5' U R 24 " pdb=" C4' U R 24 " pdb=" O4' U R 24 " ideal model delta sigma weight residual 109.10 97.00 12.10 1.50e+00 4.44e-01 6.50e+01 angle pdb=" F2 BEF c 503 " pdb=" BE BEF c 503 " pdb=" F3 BEF c 503 " ideal model delta sigma weight residual 119.96 107.09 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" F2 BEF b1002 " pdb=" BE BEF b1002 " pdb=" F3 BEF b1002 " ideal model delta sigma weight residual 119.96 107.18 12.78 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF c 504 " pdb=" BE BEF c 504 " pdb=" F3 BEF c 504 " ideal model delta sigma weight residual 119.96 107.28 12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 71213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 31080 34.04 - 68.08: 957 68.08 - 102.12: 73 102.12 - 136.16: 3 136.16 - 170.20: 5 Dihedral angle restraints: 32118 sinusoidal: 13920 harmonic: 18198 Sorted by residual: dihedral pdb=" O1B ADP c 501 " pdb=" O3A ADP c 501 " pdb=" PB ADP c 501 " pdb=" PA ADP c 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.63 145.37 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PB ADP b1000 " pdb=" PA ADP b1000 " ideal model delta sinusoidal sigma weight residual 300.00 161.68 138.32 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O2A ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PA ADP b1000 " pdb=" PB ADP b1000 " ideal model delta sinusoidal sigma weight residual -60.00 59.31 -119.31 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 32115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 8150 0.208 - 0.415: 0 0.415 - 0.623: 0 0.623 - 0.831: 0 0.831 - 1.039: 1 Chirality restraints: 8151 Sorted by residual: chirality pdb=" C4' U R 24 " pdb=" C5' U R 24 " pdb=" O4' U R 24 " pdb=" C3' U R 24 " both_signs ideal model delta sigma weight residual False -2.50 -3.54 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" C1' C R 21 " pdb=" O4' C R 21 " pdb=" C2' C R 21 " pdb=" N1 C R 21 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 8148 not shown) Planarity restraints: 9004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C R 21 " 0.033 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" N1 C R 21 " -0.037 2.00e-02 2.50e+03 pdb=" C2 C R 21 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C R 21 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C R 21 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C R 21 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C R 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C R 21 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C R 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG L 19 " -0.012 2.00e-02 2.50e+03 1.34e-02 5.35e+00 pdb=" N9 DG L 19 " 0.006 2.00e-02 2.50e+03 pdb=" C8 DG L 19 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG L 19 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG L 19 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG L 19 " 0.031 2.00e-02 2.50e+03 pdb=" O6 DG L 19 " -0.031 2.00e-02 2.50e+03 pdb=" N1 DG L 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG L 19 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG L 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG L 19 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP a 233 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" CG ASP a 233 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP a 233 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP a 233 " -0.012 2.00e-02 2.50e+03 ... (remaining 9001 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 545 2.54 - 3.13: 40532 3.13 - 3.72: 84050 3.72 - 4.31: 112364 4.31 - 4.90: 179088 Nonbonded interactions: 416579 Sorted by model distance: nonbonded pdb=" F3 BEF c 504 " pdb="MG MG d1001 " model vdw 1.950 2.120 nonbonded pdb=" O3B ADP c 501 " pdb="MG MG c 502 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR d 185 " pdb="MG MG d1001 " model vdw 1.983 2.170 nonbonded pdb=" O1B ADP a1000 " pdb="MG MG a1001 " model vdw 2.006 2.170 nonbonded pdb="MG MG c 502 " pdb=" O HOH c 603 " model vdw 2.014 2.170 ... (remaining 416574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 96 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 32003 2.51 5 N 9111 2.21 5 O 10104 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.550 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: 0.060 Extract box with map and model: 10.980 Check model and map are aligned: 0.770 Convert atoms to be neutral: 0.380 Process input model: 150.460 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.003 0.360 52482 Z= 0.218 Angle : 0.603 17.649 71218 Z= 0.336 Chirality : 0.042 1.039 8151 Planarity : 0.003 0.045 9004 Dihedral : 15.517 170.196 20372 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -2.77 (0.09), residues: 6306 helix: -1.07 (0.10), residues: 2350 sheet: -1.42 (0.16), residues: 790 loop : -2.59 (0.09), residues: 3166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 377 time to evaluate : 6.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 46 residues processed: 563 average time/residue: 0.6498 time to fit residues: 609.0026 Evaluate side-chains 306 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 6.725 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4568 time to fit residues: 48.0732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 6.9990 chunk 479 optimal weight: 8.9990 chunk 266 optimal weight: 30.0000 chunk 163 optimal weight: 0.0170 chunk 323 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 496 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 chunk 369 optimal weight: 6.9990 chunk 574 optimal weight: 30.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 190 ASN ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 344 HIS ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 275 ASN b 25 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS d 42 HIS ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS A 41 GLN A 303 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN X 41 GLN X 343 HIS ** X 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS X 808 ASN X 832 HIS X1008 GLN X1010 GLN X1013 GLN X1017 GLN X1209 GLN X1236 ASN X1237 HIS X1257 GLN X1268 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 489 ASN ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1114 GLN Y1244 GLN ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1367 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 52482 Z= 0.216 Angle : 0.575 10.308 71218 Z= 0.287 Chirality : 0.041 0.262 8151 Planarity : 0.004 0.049 9004 Dihedral : 10.810 174.723 7862 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -1.56 (0.10), residues: 6306 helix: 0.17 (0.11), residues: 2351 sheet: -0.97 (0.17), residues: 786 loop : -2.03 (0.10), residues: 3169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 261 time to evaluate : 6.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 19 residues processed: 297 average time/residue: 0.6553 time to fit residues: 329.2748 Evaluate side-chains 253 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 234 time to evaluate : 6.755 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5121 time to fit residues: 25.7995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 478 optimal weight: 2.9990 chunk 391 optimal weight: 0.0870 chunk 158 optimal weight: 6.9990 chunk 575 optimal weight: 0.0070 chunk 622 optimal weight: 2.9990 chunk 512 optimal weight: 4.9990 chunk 571 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS f 140 HIS f 142 ASN ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 275 ASN a 90 ASN a 142 ASN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN b 142 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 142 ASN ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 142 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 275 ASN e 25 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 GLN X1009 ASN X1288 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 52482 Z= 0.163 Angle : 0.537 10.393 71218 Z= 0.267 Chirality : 0.040 0.189 8151 Planarity : 0.003 0.052 9004 Dihedral : 10.774 177.050 7862 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -1.04 (0.10), residues: 6306 helix: 0.58 (0.11), residues: 2354 sheet: -0.68 (0.17), residues: 797 loop : -1.72 (0.11), residues: 3155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 6.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 267 average time/residue: 0.6587 time to fit residues: 301.4481 Evaluate side-chains 241 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 6.680 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.5016 time to fit residues: 20.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 386 optimal weight: 8.9990 chunk 577 optimal weight: 3.9990 chunk 611 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 547 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 HIS ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN A 70 GLN A 286 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 GLN ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 952 GLN X1017 GLN X1157 GLN Y 274 ASN Y 545 HIS Y 702 GLN Y 792 ASN Y 817 HIS ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 52482 Z= 0.380 Angle : 0.698 12.515 71218 Z= 0.356 Chirality : 0.042 0.207 8151 Planarity : 0.004 0.055 9004 Dihedral : 11.104 179.149 7862 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -1.09 (0.10), residues: 6306 helix: 0.35 (0.11), residues: 2417 sheet: -0.65 (0.17), residues: 793 loop : -1.63 (0.11), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 228 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 30 residues processed: 296 average time/residue: 0.6208 time to fit residues: 316.2707 Evaluate side-chains 247 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 6.762 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.5197 time to fit residues: 36.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 522 optimal weight: 8.9990 chunk 422 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 549 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 275 ASN ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 344 HIS ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 52482 Z= 0.235 Angle : 0.594 12.052 71218 Z= 0.299 Chirality : 0.041 0.281 8151 Planarity : 0.003 0.057 9004 Dihedral : 10.993 179.547 7862 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.88 (0.10), residues: 6306 helix: 0.56 (0.11), residues: 2387 sheet: -0.52 (0.18), residues: 788 loop : -1.52 (0.11), residues: 3131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 6.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 17 residues processed: 267 average time/residue: 0.6399 time to fit residues: 295.4689 Evaluate side-chains 228 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 6.524 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5375 time to fit residues: 24.5332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 10.0000 chunk 551 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 612 optimal weight: 9.9990 chunk 508 optimal weight: 3.9990 chunk 283 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 202 optimal weight: 0.4980 chunk 321 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 517 GLN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 52482 Z= 0.206 Angle : 0.594 13.009 71218 Z= 0.294 Chirality : 0.041 0.237 8151 Planarity : 0.003 0.055 9004 Dihedral : 10.925 179.062 7862 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.69 (0.11), residues: 6306 helix: 0.67 (0.11), residues: 2385 sheet: -0.44 (0.18), residues: 793 loop : -1.37 (0.11), residues: 3128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 250 average time/residue: 0.6230 time to fit residues: 271.4151 Evaluate side-chains 226 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 8.087 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5196 time to fit residues: 24.6229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 348 optimal weight: 6.9990 chunk 447 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 chunk 515 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 610 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 281 optimal weight: 30.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 276 HIS ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 52482 Z= 0.320 Angle : 0.684 13.616 71218 Z= 0.342 Chirality : 0.042 0.267 8151 Planarity : 0.004 0.055 9004 Dihedral : 11.163 169.251 7862 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.82 (0.11), residues: 6306 helix: 0.49 (0.11), residues: 2417 sheet: -0.55 (0.18), residues: 794 loop : -1.38 (0.11), residues: 3095 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 254 average time/residue: 0.6393 time to fit residues: 279.5097 Evaluate side-chains 228 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 6.749 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5824 time to fit residues: 28.9773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 387 optimal weight: 0.0040 chunk 415 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 479 optimal weight: 5.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 HIS U 147 GLN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 52482 Z= 0.266 Angle : 0.656 13.803 71218 Z= 0.324 Chirality : 0.042 0.283 8151 Planarity : 0.004 0.057 9004 Dihedral : 11.147 154.291 7862 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.68 (0.11), residues: 6306 helix: 0.60 (0.11), residues: 2383 sheet: -0.56 (0.18), residues: 766 loop : -1.24 (0.11), residues: 3157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 224 average time/residue: 0.6144 time to fit residues: 241.1467 Evaluate side-chains 213 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 5.849 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5368 time to fit residues: 14.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.0020 chunk 584 optimal weight: 20.0000 chunk 533 optimal weight: 6.9990 chunk 568 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 446 optimal weight: 0.0870 chunk 174 optimal weight: 0.5980 chunk 513 optimal weight: 0.8980 chunk 537 optimal weight: 6.9990 chunk 566 optimal weight: 3.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS f 172 GLN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 GLN b 344 HIS c 172 GLN c 275 ASN ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 52482 Z= 0.154 Angle : 0.638 17.366 71218 Z= 0.307 Chirality : 0.042 0.288 8151 Planarity : 0.003 0.060 9004 Dihedral : 10.893 148.027 7862 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.53 (0.11), residues: 6306 helix: 0.69 (0.11), residues: 2404 sheet: -0.33 (0.18), residues: 808 loop : -1.18 (0.12), residues: 3094 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 6.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 226 average time/residue: 0.6362 time to fit residues: 248.2959 Evaluate side-chains 216 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 6.179 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4547 time to fit residues: 9.8841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 8.9990 chunk 601 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 417 optimal weight: 0.0970 chunk 630 optimal weight: 10.0000 chunk 580 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 387 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 667 GLN ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 52482 Z= 0.177 Angle : 0.638 15.686 71218 Z= 0.309 Chirality : 0.041 0.299 8151 Planarity : 0.003 0.076 9004 Dihedral : 10.851 145.142 7862 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % 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: -0.39 (0.11), residues: 6306 helix: 0.78 (0.11), residues: 2382 sheet: -0.21 (0.18), residues: 818 loop : -1.09 (0.12), residues: 3106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 5.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 217 average time/residue: 0.6448 time to fit residues: 245.8103 Evaluate side-chains 210 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 6.076 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4997 time to fit residues: 10.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 7.9990 chunk 534 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 502 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 chunk 516 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.038333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.024678 restraints weight = 641428.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.025075 restraints weight = 367353.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.025511 restraints weight = 255458.679| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 52482 Z= 0.267 Angle : 0.700 15.312 71218 Z= 0.341 Chirality : 0.042 0.314 8151 Planarity : 0.004 0.067 9004 Dihedral : 11.059 145.764 7862 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.39 (0.11), residues: 6306 helix: 0.80 (0.11), residues: 2309 sheet: -0.29 (0.18), residues: 820 loop : -1.03 (0.11), residues: 3177 =============================================================================== Job complete usr+sys time: 8298.53 seconds wall clock time: 152 minutes 40.54 seconds (9160.54 seconds total)