Starting phenix.real_space_refine on Sun Feb 25 12:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/02_2024/7adc_11723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/02_2024/7adc_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_11723/02_2024/7adc_11723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/02_2024/7adc_11723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/02_2024/7adc_11723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/02_2024/7adc_11723_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 25.72, per 1000 atoms: 0.50 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: 20.58 Conformation dependent library (CDL) restraints added in 8.5 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: 21.01 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: 21.58 Time building geometry restraints manager: 22.11 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: 31154 34.04 - 68.08: 1020 68.08 - 102.12: 84 102.12 - 136.16: 3 136.16 - 170.20: 5 Dihedral angle restraints: 32266 sinusoidal: 14068 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 32263 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 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: 1.530 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: 8.480 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 145.960 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 15.845 170.196 20520 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.78 % Allowed : 6.27 % Favored : 89.94 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 381 HIS 0.005 0.001 HIS Y1366 PHE 0.027 0.001 PHE Y 227 TYR 0.007 0.001 TYR Y 631 ARG 0.007 0.000 ARG b 353 *********************** 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 : 6.164 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 REVERT: f 21 MET cc_start: 0.6072 (mmm) cc_final: 0.5436 (mtt) REVERT: f 98 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (p) REVERT: f 207 LEU cc_start: 0.8413 (tp) cc_final: 0.7876 (tt) REVERT: f 210 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: f 343 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (mt) REVERT: a 210 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (t0) REVERT: a 245 MET cc_start: 0.8271 (tpp) cc_final: 0.7901 (tpt) REVERT: a 281 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6251 (p) REVERT: b 59 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: b 245 MET cc_start: 0.7767 (tpp) cc_final: 0.7476 (tpp) REVERT: b 281 SER cc_start: 0.7051 (OUTLIER) cc_final: 0.6846 (p) REVERT: d 59 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: d 230 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7376 (p) REVERT: d 245 MET cc_start: 0.7711 (tpp) cc_final: 0.6821 (tpp) REVERT: d 281 SER cc_start: 0.7340 (OUTLIER) cc_final: 0.7030 (p) REVERT: e 281 SER cc_start: 0.4919 (OUTLIER) cc_final: 0.4551 (p) REVERT: e 380 MET cc_start: 0.8972 (mtp) cc_final: 0.8674 (mtp) REVERT: U 86 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7424 (ttpp) REVERT: U 137 ASN cc_start: 0.7891 (p0) cc_final: 0.7496 (p0) REVERT: W 30 MET cc_start: 0.8311 (mmt) cc_final: 0.7970 (mmt) REVERT: X 842 ASP cc_start: 0.7570 (t0) cc_final: 0.7349 (t0) REVERT: Y 697 MET cc_start: 0.8159 (tmm) cc_final: 0.7711 (tmm) REVERT: Y 698 MET cc_start: 0.8193 (tpp) cc_final: 0.7890 (tpp) REVERT: Y 1040 MET cc_start: 0.7014 (ttm) cc_final: 0.6722 (ttt) outliers start: 204 outliers final: 46 residues processed: 563 average time/residue: 0.6477 time to fit residues: 604.6563 Evaluate side-chains 319 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 5.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 98 SER Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 210 ASP Chi-restraints excluded: chain f residue 281 SER Chi-restraints excluded: chain f residue 329 GLU Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain f residue 346 SER Chi-restraints excluded: chain f residue 369 GLU Chi-restraints excluded: chain f residue 373 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 210 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 281 SER Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 369 GLU Chi-restraints excluded: chain b residue 16 THR Chi-restraints excluded: chain b residue 32 GLN Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 281 SER Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 369 GLU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 228 VAL Chi-restraints excluded: chain c residue 277 VAL Chi-restraints excluded: chain c residue 281 SER Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 369 GLU Chi-restraints excluded: chain c residue 373 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 59 GLN Chi-restraints excluded: chain d residue 166 SER Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 230 SER Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain d residue 281 SER Chi-restraints excluded: chain d residue 323 THR Chi-restraints excluded: chain d residue 329 GLU Chi-restraints excluded: chain d residue 369 GLU Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 281 SER Chi-restraints excluded: chain e residue 323 THR Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain e residue 369 GLU Chi-restraints excluded: chain e residue 373 THR 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: 3.9990 chunk 266 optimal weight: 20.0000 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: 8.9990 chunk 301 optimal weight: 0.9990 chunk 369 optimal weight: 8.9990 chunk 574 optimal weight: 30.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- 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 42 HIS a 90 ASN ** 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 42 HIS ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** b 275 ASN ** 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 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 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 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 ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS X 808 ASN X 832 HIS X1008 GLN X1009 ASN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 702 GLN ** 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 52482 Z= 0.253 Angle : 0.601 10.761 71218 Z= 0.304 Chirality : 0.041 0.199 8151 Planarity : 0.004 0.060 9004 Dihedral : 12.497 176.322 8095 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.28 % Allowed : 12.76 % Favored : 85.96 % 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: -1.48 (0.10), residues: 6306 helix: 0.23 (0.11), residues: 2353 sheet: -0.88 (0.17), residues: 793 loop : -1.99 (0.10), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 997 HIS 0.004 0.001 HIS Y 104 PHE 0.018 0.001 PHE X 195 TYR 0.023 0.001 TYR c 274 ARG 0.016 0.001 ARG V 235 *********************** 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 326 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 257 time to evaluate : 5.556 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: f 21 MET cc_start: 0.5811 (mmm) cc_final: 0.5082 (mtt) REVERT: f 147 MET cc_start: 0.8832 (tpp) cc_final: 0.8587 (tpt) REVERT: f 207 LEU cc_start: 0.8499 (tp) cc_final: 0.8253 (tp) REVERT: f 390 MET cc_start: 0.7489 (ptp) cc_final: 0.6991 (ptt) REVERT: a 147 MET cc_start: 0.8890 (tpp) cc_final: 0.8534 (tpp) REVERT: a 326 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (ptmm) REVERT: a 396 MET cc_start: 0.8614 (mmm) cc_final: 0.8330 (mmm) REVERT: b 219 MET cc_start: 0.8076 (mpp) cc_final: 0.7805 (mmp) REVERT: b 390 MET cc_start: 0.7317 (ptp) cc_final: 0.6478 (ptp) REVERT: c 1 MET cc_start: 0.7626 (ptm) cc_final: 0.6693 (ppp) REVERT: d 21 MET cc_start: 0.8501 (mmm) cc_final: 0.6282 (ptt) REVERT: d 245 MET cc_start: 0.7740 (tpp) cc_final: 0.7512 (tpp) REVERT: e 380 MET cc_start: 0.9094 (mtp) cc_final: 0.8734 (mtp) REVERT: U 137 ASN cc_start: 0.8019 (p0) cc_final: 0.7804 (p0) REVERT: W 30 MET cc_start: 0.8573 (mmt) cc_final: 0.8330 (mmt) REVERT: W 36 ASP cc_start: 0.8447 (p0) cc_final: 0.8212 (p0) REVERT: X 124 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7911 (ppp) REVERT: X 741 MET cc_start: 0.8475 (tpp) cc_final: 0.8233 (tpp) REVERT: X 842 ASP cc_start: 0.7751 (t0) cc_final: 0.7471 (t0) REVERT: Y 372 MET cc_start: 0.7766 (mmt) cc_final: 0.7176 (mmt) outliers start: 69 outliers final: 32 residues processed: 313 average time/residue: 0.6398 time to fit residues: 336.4803 Evaluate side-chains 269 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 5.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 286 THR Chi-restraints excluded: chain f residue 326 LYS Chi-restraints excluded: chain f residue 373 THR Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 411 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 286 THR Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain c residue 373 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 323 THR Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 323 THR Chi-restraints excluded: chain e residue 416 MET Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 853 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 0.4980 chunk 178 optimal weight: 10.0000 chunk 478 optimal weight: 7.9990 chunk 391 optimal weight: 0.0370 chunk 158 optimal weight: 6.9990 chunk 575 optimal weight: 9.9990 chunk 622 optimal weight: 1.9990 chunk 512 optimal weight: 7.9990 chunk 571 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 overall best weight: 3.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 ASN f 172 GLN ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** 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 142 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 275 ASN e 142 ASN ** e 172 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 517 GLN X 658 GLN X1010 GLN 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 817 HIS ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 52482 Z= 0.204 Angle : 0.550 10.631 71218 Z= 0.277 Chirality : 0.040 0.191 8151 Planarity : 0.003 0.052 9004 Dihedral : 12.004 178.058 8023 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.22 % Allowed : 15.14 % Favored : 83.64 % 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: -0.96 (0.11), residues: 6306 helix: 0.64 (0.11), residues: 2363 sheet: -0.80 (0.17), residues: 801 loop : -1.61 (0.11), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 381 HIS 0.004 0.001 HIS d 42 PHE 0.026 0.001 PHE U 231 TYR 0.027 0.001 TYR e 72 ARG 0.008 0.000 ARG W 69 *********************** 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 305 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 5.816 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: f 21 MET cc_start: 0.5742 (mmm) cc_final: 0.4961 (mtt) REVERT: f 29 MET cc_start: -0.2219 (ptt) cc_final: -0.2427 (pmm) REVERT: f 207 LEU cc_start: 0.8530 (tp) cc_final: 0.8280 (tp) REVERT: f 380 MET cc_start: 0.8898 (ptp) cc_final: 0.8108 (ptp) REVERT: f 390 MET cc_start: 0.7826 (ptp) cc_final: 0.7269 (ptt) REVERT: a 147 MET cc_start: 0.8943 (tpp) cc_final: 0.8394 (tpp) REVERT: a 207 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8397 (mt) REVERT: a 219 MET cc_start: 0.8601 (mmt) cc_final: 0.8142 (mmm) REVERT: a 416 MET cc_start: 0.9307 (mmm) cc_final: 0.8902 (mmt) REVERT: b 1 MET cc_start: 0.7765 (ptm) cc_final: 0.7225 (ppp) REVERT: b 147 MET cc_start: 0.8832 (tpp) cc_final: 0.8589 (tpp) REVERT: b 390 MET cc_start: 0.7366 (ptp) cc_final: 0.6677 (ptp) REVERT: c 1 MET cc_start: 0.7635 (ptm) cc_final: 0.6811 (ppp) REVERT: c 21 MET cc_start: 0.7125 (mtp) cc_final: 0.6005 (ptp) REVERT: d 21 MET cc_start: 0.8537 (mmm) cc_final: 0.6287 (ptt) REVERT: d 245 MET cc_start: 0.7857 (tpp) cc_final: 0.7593 (tpp) REVERT: e 380 MET cc_start: 0.9085 (mtp) cc_final: 0.8650 (mtp) REVERT: A 43 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7701 (tp) REVERT: U 137 ASN cc_start: 0.8088 (p0) cc_final: 0.7855 (p0) REVERT: W 30 MET cc_start: 0.8586 (mmt) cc_final: 0.8347 (mmt) REVERT: W 36 ASP cc_start: 0.8548 (p0) cc_final: 0.8306 (p0) REVERT: X 130 MET cc_start: 0.7751 (ptp) cc_final: 0.7389 (ptp) REVERT: X 403 MET cc_start: 0.7920 (tmm) cc_final: 0.7677 (tmm) REVERT: X 842 ASP cc_start: 0.7782 (t0) cc_final: 0.7498 (t0) REVERT: Y 932 MET cc_start: 0.7755 (mmm) cc_final: 0.7231 (mtt) REVERT: Y 1040 MET cc_start: 0.6775 (ttt) cc_final: 0.6475 (ttt) REVERT: Y 1189 MET cc_start: 0.8890 (mmm) cc_final: 0.7907 (tpp) outliers start: 66 outliers final: 37 residues processed: 296 average time/residue: 0.6092 time to fit residues: 311.4147 Evaluate side-chains 266 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 142 ASN Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 373 THR Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 346 SER Chi-restraints excluded: chain a residue 411 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 373 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 207 LEU Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 343 LEU Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 416 MET Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 1290 MET Chi-restraints excluded: chain Y residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 63 optimal weight: 0.0170 chunk 274 optimal weight: 0.8980 chunk 386 optimal weight: 0.0570 chunk 577 optimal weight: 20.0000 chunk 611 optimal weight: 0.0770 chunk 301 optimal weight: 7.9990 chunk 547 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 GLN f 275 ASN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 275 ASN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 142 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 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 73 GLN X 658 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 792 ASN ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 52482 Z= 0.147 Angle : 0.528 10.962 71218 Z= 0.261 Chirality : 0.040 0.196 8151 Planarity : 0.003 0.054 9004 Dihedral : 11.857 176.460 8017 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.22 % Allowed : 16.59 % Favored : 82.19 % 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: -0.72 (0.11), residues: 6306 helix: 0.80 (0.11), residues: 2348 sheet: -0.58 (0.17), residues: 805 loop : -1.46 (0.11), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 997 HIS 0.005 0.001 HIS d 140 PHE 0.009 0.001 PHE X 195 TYR 0.015 0.001 TYR e 72 ARG 0.006 0.000 ARG W 69 *********************** 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 296 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 6.099 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: f 21 MET cc_start: 0.5865 (mmm) cc_final: 0.4991 (mtp) REVERT: f 147 MET cc_start: 0.8345 (tpt) cc_final: 0.7359 (tpp) REVERT: f 207 LEU cc_start: 0.8454 (tp) cc_final: 0.8203 (tp) REVERT: f 390 MET cc_start: 0.7806 (ptp) cc_final: 0.7273 (ptt) REVERT: f 405 MET cc_start: 0.8729 (ptp) cc_final: 0.7900 (ppp) REVERT: f 416 MET cc_start: 0.8979 (mmm) cc_final: 0.8441 (mmm) REVERT: a 1 MET cc_start: 0.6997 (ppp) cc_final: 0.6764 (ppp) REVERT: a 147 MET cc_start: 0.8997 (tpp) cc_final: 0.8518 (tpp) REVERT: a 416 MET cc_start: 0.9238 (mmm) cc_final: 0.8942 (mmt) REVERT: b 1 MET cc_start: 0.7869 (ptm) cc_final: 0.7523 (ppp) REVERT: b 390 MET cc_start: 0.7548 (ptp) cc_final: 0.6909 (ptp) REVERT: c 1 MET cc_start: 0.7521 (ptm) cc_final: 0.6812 (ppp) REVERT: c 21 MET cc_start: 0.7152 (mtp) cc_final: 0.5723 (ptp) REVERT: c 327 MET cc_start: 0.8364 (ppp) cc_final: 0.8131 (ppp) REVERT: d 21 MET cc_start: 0.8500 (mmm) cc_final: 0.6216 (ptt) REVERT: d 245 MET cc_start: 0.7927 (tpp) cc_final: 0.7657 (tpp) REVERT: e 186 MET cc_start: 0.8322 (pmm) cc_final: 0.8068 (pmm) REVERT: e 341 MET cc_start: 0.9095 (tpt) cc_final: 0.8855 (tpt) REVERT: e 390 MET cc_start: 0.7339 (pmm) cc_final: 0.7064 (pmm) REVERT: A 57 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8527 (p0) REVERT: A 167 MET cc_start: 0.4435 (ptp) cc_final: 0.4138 (ptp) REVERT: A 305 MET cc_start: -0.3605 (ttp) cc_final: -0.3846 (ttt) REVERT: U 137 ASN cc_start: 0.8041 (p0) cc_final: 0.7814 (p0) REVERT: W 30 MET cc_start: 0.8583 (mmt) cc_final: 0.8333 (mmt) REVERT: W 36 ASP cc_start: 0.8524 (p0) cc_final: 0.8320 (p0) REVERT: W 72 GLN cc_start: 0.9343 (tp-100) cc_final: 0.9103 (tp-100) REVERT: X 124 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7794 (ppp) REVERT: X 130 MET cc_start: 0.7639 (ptp) cc_final: 0.7354 (ptp) REVERT: X 741 MET cc_start: 0.8579 (tpp) cc_final: 0.8341 (tpp) REVERT: X 842 ASP cc_start: 0.7673 (t0) cc_final: 0.7390 (t0) REVERT: X 1119 MET cc_start: 0.7836 (tpp) cc_final: 0.7554 (tpp) REVERT: X 1243 MET cc_start: 0.7724 (tmm) cc_final: 0.6903 (tmm) REVERT: Y 151 MET cc_start: 0.9005 (ppp) cc_final: 0.8694 (ppp) REVERT: Y 697 MET cc_start: 0.7902 (ttp) cc_final: 0.7669 (ttp) REVERT: Y 1189 MET cc_start: 0.8864 (mmm) cc_final: 0.7956 (tpp) outliers start: 66 outliers final: 31 residues processed: 288 average time/residue: 0.6395 time to fit residues: 318.1754 Evaluate side-chains 258 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 5.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 346 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 1290 MET Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 953 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 455 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 522 optimal weight: 0.0170 chunk 422 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 549 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 172 GLN b 142 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 172 GLN c 275 ASN d 142 ASN ** d 172 GLN ** 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** V 147 GLN X 165 HIS Y 488 ASN ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 52482 Z= 0.129 Angle : 0.533 12.308 71218 Z= 0.260 Chirality : 0.040 0.204 8151 Planarity : 0.003 0.054 9004 Dihedral : 11.738 177.646 8014 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.21 % Allowed : 17.01 % Favored : 81.78 % 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: -0.57 (0.11), residues: 6306 helix: 0.85 (0.11), residues: 2351 sheet: -0.40 (0.18), residues: 797 loop : -1.33 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 381 HIS 0.004 0.000 HIS d 140 PHE 0.007 0.001 PHE Y 719 TYR 0.011 0.001 TYR Y 631 ARG 0.003 0.000 ARG W 69 *********************** 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 298 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 233 time to evaluate : 5.737 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: f 21 MET cc_start: 0.6063 (mmm) cc_final: 0.5302 (mtt) REVERT: f 207 LEU cc_start: 0.8450 (tp) cc_final: 0.8194 (tp) REVERT: f 390 MET cc_start: 0.7949 (ptp) cc_final: 0.7419 (ptt) REVERT: a 147 MET cc_start: 0.8998 (tpp) cc_final: 0.8542 (tpp) REVERT: a 219 MET cc_start: 0.8431 (mmt) cc_final: 0.8220 (mmm) REVERT: a 326 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8583 (ptmm) REVERT: a 416 MET cc_start: 0.9200 (mmm) cc_final: 0.8926 (mmt) REVERT: b 1 MET cc_start: 0.7732 (ptm) cc_final: 0.7528 (ppp) REVERT: b 147 MET cc_start: 0.8831 (tpp) cc_final: 0.8606 (tpp) REVERT: c 1 MET cc_start: 0.7507 (ptm) cc_final: 0.6919 (ppp) REVERT: c 21 MET cc_start: 0.7023 (mtp) cc_final: 0.5799 (ptp) REVERT: d 21 MET cc_start: 0.8383 (mmm) cc_final: 0.6039 (ptt) REVERT: d 245 MET cc_start: 0.7788 (tpp) cc_final: 0.7515 (tpp) REVERT: e 1 MET cc_start: 0.6831 (ppp) cc_final: 0.6617 (ppp) REVERT: e 186 MET cc_start: 0.8333 (pmm) cc_final: 0.8050 (pmm) REVERT: e 341 MET cc_start: 0.9130 (tpt) cc_final: 0.8858 (tpt) REVERT: e 380 MET cc_start: 0.9181 (ptp) cc_final: 0.8754 (ppp) REVERT: e 390 MET cc_start: 0.7250 (pmm) cc_final: 0.6989 (pmm) REVERT: A 57 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8464 (p0) REVERT: U 137 ASN cc_start: 0.8051 (p0) cc_final: 0.7843 (p0) REVERT: W 72 GLN cc_start: 0.9370 (tp-100) cc_final: 0.9111 (tp-100) REVERT: X 124 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7704 (ppp) REVERT: X 130 MET cc_start: 0.7599 (ptp) cc_final: 0.7334 (ptp) REVERT: X 842 ASP cc_start: 0.7585 (t0) cc_final: 0.7283 (t0) REVERT: X 1290 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7445 (mmp) REVERT: Y 151 MET cc_start: 0.8927 (ppp) cc_final: 0.8594 (pmm) REVERT: Y 180 MET cc_start: 0.3876 (tpt) cc_final: 0.2763 (tpt) REVERT: Y 513 MET cc_start: 0.7807 (mmm) cc_final: 0.7563 (mtt) REVERT: Y 1189 MET cc_start: 0.8887 (mmm) cc_final: 0.7933 (tpp) outliers start: 65 outliers final: 33 residues processed: 287 average time/residue: 0.6375 time to fit residues: 314.6413 Evaluate side-chains 262 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 1290 MET Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 953 LYS Chi-restraints excluded: chain Y residue 974 VAL 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: 1.9990 chunk 120 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 612 optimal weight: 1.9990 chunk 508 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 50 optimal weight: 0.0070 chunk 202 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN c 172 GLN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 344 HIS ** 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** V 147 GLN ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 52482 Z= 0.160 Angle : 0.545 13.134 71218 Z= 0.266 Chirality : 0.040 0.216 8151 Planarity : 0.003 0.056 9004 Dihedral : 11.728 179.962 8012 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.24 % Allowed : 17.87 % Favored : 80.89 % 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: -0.43 (0.11), residues: 6306 helix: 0.97 (0.11), residues: 2347 sheet: -0.32 (0.18), residues: 814 loop : -1.25 (0.11), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 381 HIS 0.005 0.001 HIS d 140 PHE 0.024 0.001 PHE U 231 TYR 0.036 0.001 TYR X1229 ARG 0.010 0.000 ARG f 221 *********************** 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 297 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 230 time to evaluate : 5.675 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: f 21 MET cc_start: 0.6074 (mmm) cc_final: 0.5303 (mtt) REVERT: f 207 LEU cc_start: 0.8476 (tp) cc_final: 0.8206 (tp) REVERT: f 390 MET cc_start: 0.7986 (ptp) cc_final: 0.7522 (ptt) REVERT: f 416 MET cc_start: 0.8739 (mmm) cc_final: 0.8533 (mmm) REVERT: a 147 MET cc_start: 0.9107 (tpp) cc_final: 0.8631 (tpp) REVERT: a 416 MET cc_start: 0.9216 (mmm) cc_final: 0.8955 (mmt) REVERT: b 1 MET cc_start: 0.7972 (ptm) cc_final: 0.7716 (ppp) REVERT: b 21 MET cc_start: 0.6399 (ptt) cc_final: 0.6084 (ptt) REVERT: b 29 MET cc_start: 0.6760 (mpp) cc_final: 0.5777 (pmm) REVERT: b 147 MET cc_start: 0.8920 (tpp) cc_final: 0.8511 (tpp) REVERT: c 1 MET cc_start: 0.7585 (ptm) cc_final: 0.6941 (ppp) REVERT: c 21 MET cc_start: 0.7152 (mtp) cc_final: 0.6054 (ptp) REVERT: d 21 MET cc_start: 0.8416 (mmm) cc_final: 0.6081 (ptt) REVERT: d 142 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8293 (m-40) REVERT: d 245 MET cc_start: 0.7961 (tpp) cc_final: 0.7443 (mmt) REVERT: d 405 MET cc_start: 0.8426 (pmm) cc_final: 0.8168 (pmm) REVERT: e 186 MET cc_start: 0.8401 (pmm) cc_final: 0.8103 (pmm) REVERT: A 43 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7721 (tp) REVERT: A 57 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8530 (p0) REVERT: U 137 ASN cc_start: 0.7987 (p0) cc_final: 0.7762 (p0) REVERT: W 72 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9053 (tp-100) REVERT: X 124 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7876 (ppp) REVERT: X 130 MET cc_start: 0.7622 (ptp) cc_final: 0.7390 (ptp) REVERT: X 403 MET cc_start: 0.7925 (tmm) cc_final: 0.7632 (tmm) REVERT: X 842 ASP cc_start: 0.7628 (t0) cc_final: 0.7333 (t0) REVERT: Y 130 MET cc_start: 0.7522 (ppp) cc_final: 0.6836 (ppp) REVERT: Y 180 MET cc_start: 0.4267 (tpt) cc_final: 0.3430 (tpt) outliers start: 67 outliers final: 43 residues processed: 288 average time/residue: 0.6414 time to fit residues: 319.4863 Evaluate side-chains 270 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1287 LEU Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 953 LYS Chi-restraints excluded: chain Y residue 974 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 0.2980 chunk 69 optimal weight: 0.0980 chunk 348 optimal weight: 2.9990 chunk 447 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 515 optimal weight: 30.0000 chunk 341 optimal weight: 40.0000 chunk 610 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- 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** ** b 42 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** d 42 HIS ** 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 70 GLN ** 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 490 GLN X 952 GLN X1017 GLN ** Y 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 52482 Z= 0.220 Angle : 0.592 13.525 71218 Z= 0.293 Chirality : 0.040 0.238 8151 Planarity : 0.003 0.054 9004 Dihedral : 11.847 176.731 8012 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 18.27 % Favored : 80.33 % 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: -0.32 (0.11), residues: 6306 helix: 1.04 (0.11), residues: 2331 sheet: -0.20 (0.18), residues: 809 loop : -1.17 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 381 HIS 0.006 0.001 HIS X 165 PHE 0.010 0.001 PHE d 355 TYR 0.030 0.001 TYR X1229 ARG 0.012 0.000 ARG Y 905 *********************** 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 300 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 6.131 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: f 21 MET cc_start: 0.5859 (mmm) cc_final: 0.5186 (mtt) REVERT: f 147 MET cc_start: 0.8306 (tpt) cc_final: 0.7421 (tpp) REVERT: f 390 MET cc_start: 0.8036 (ptp) cc_final: 0.7559 (ptt) REVERT: f 416 MET cc_start: 0.8916 (mmm) cc_final: 0.8518 (mmm) REVERT: a 1 MET cc_start: 0.7202 (ppp) cc_final: 0.6994 (ppp) REVERT: a 219 MET cc_start: 0.8566 (mmt) cc_final: 0.8171 (mmm) REVERT: a 416 MET cc_start: 0.9273 (mmm) cc_final: 0.9005 (mmt) REVERT: b 1 MET cc_start: 0.8340 (ptm) cc_final: 0.7970 (ppp) REVERT: b 405 MET cc_start: 0.9178 (ptp) cc_final: 0.8843 (ptp) REVERT: c 1 MET cc_start: 0.7650 (ptm) cc_final: 0.7008 (ppp) REVERT: c 390 MET cc_start: 0.6449 (ptt) cc_final: 0.5765 (ppp) REVERT: d 21 MET cc_start: 0.8435 (mmm) cc_final: 0.6251 (ptt) REVERT: d 245 MET cc_start: 0.8087 (tpp) cc_final: 0.7535 (mmt) REVERT: d 405 MET cc_start: 0.8608 (pmm) cc_final: 0.8380 (pmm) REVERT: e 186 MET cc_start: 0.8485 (pmm) cc_final: 0.8166 (pmm) REVERT: e 390 MET cc_start: 0.7491 (pmm) cc_final: 0.7285 (pmm) REVERT: A 43 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 57 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8495 (p0) REVERT: U 137 ASN cc_start: 0.8143 (p0) cc_final: 0.7868 (p0) REVERT: W 30 MET cc_start: 0.8711 (tpp) cc_final: 0.8083 (mmt) REVERT: W 72 GLN cc_start: 0.9380 (tp-100) cc_final: 0.9037 (tp-100) REVERT: X 124 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8102 (ppp) REVERT: X 842 ASP cc_start: 0.7779 (t0) cc_final: 0.7438 (t0) REVERT: Y 151 MET cc_start: 0.8809 (ppp) cc_final: 0.8601 (pmm) REVERT: Y 604 MET cc_start: 0.7874 (mmm) cc_final: 0.7423 (tpp) outliers start: 75 outliers final: 55 residues processed: 293 average time/residue: 0.6093 time to fit residues: 311.3946 Evaluate side-chains 282 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain b residue 416 MET Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 194 GLN Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1227 VAL Chi-restraints excluded: chain X residue 1287 LEU Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 953 LYS Chi-restraints excluded: chain Y residue 974 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 364 optimal weight: 6.9990 chunk 183 optimal weight: 0.0010 chunk 119 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 387 optimal weight: 50.0000 chunk 415 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 479 optimal weight: 6.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- 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 42 HIS ** a 189 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 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 ASN ** 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 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** X 490 GLN ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 477 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 52482 Z= 0.262 Angle : 0.647 13.686 71218 Z= 0.318 Chirality : 0.041 0.268 8151 Planarity : 0.004 0.054 9004 Dihedral : 11.976 171.410 8012 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.48 % Allowed : 18.74 % Favored : 79.78 % 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: -0.43 (0.11), residues: 6306 helix: 0.90 (0.11), residues: 2350 sheet: -0.31 (0.18), residues: 820 loop : -1.21 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 381 HIS 0.012 0.001 HIS b 388 PHE 0.031 0.001 PHE U 231 TYR 0.026 0.002 TYR X1229 ARG 0.006 0.000 ARG W 16 *********************** 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 302 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 222 time to evaluate : 5.768 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: f 21 MET cc_start: 0.5969 (mmm) cc_final: 0.5197 (mtt) REVERT: f 147 MET cc_start: 0.8244 (tpt) cc_final: 0.7510 (tpp) REVERT: f 380 MET cc_start: 0.8662 (ptp) cc_final: 0.8308 (ptp) REVERT: f 416 MET cc_start: 0.8962 (mmm) cc_final: 0.8644 (mmm) REVERT: a 147 MET cc_start: 0.8914 (tpt) cc_final: 0.8213 (tpp) REVERT: a 219 MET cc_start: 0.8690 (mmt) cc_final: 0.8323 (mmm) REVERT: a 396 MET cc_start: 0.8637 (mmm) cc_final: 0.8036 (mmm) REVERT: a 405 MET cc_start: 0.8090 (ptp) cc_final: 0.7887 (ppp) REVERT: b 1 MET cc_start: 0.8431 (ptm) cc_final: 0.8009 (ppp) REVERT: b 21 MET cc_start: 0.6608 (ptt) cc_final: 0.5749 (tmm) REVERT: b 29 MET cc_start: 0.7078 (mpp) cc_final: 0.6181 (pmm) REVERT: b 147 MET cc_start: 0.8912 (tpp) cc_final: 0.7581 (tpp) REVERT: d 21 MET cc_start: 0.8559 (mmm) cc_final: 0.6373 (ptt) REVERT: d 245 MET cc_start: 0.8166 (tpp) cc_final: 0.7660 (mmt) REVERT: d 405 MET cc_start: 0.8505 (pmm) cc_final: 0.8299 (pmm) REVERT: e 29 MET cc_start: 0.7338 (pmm) cc_final: 0.6952 (pmm) REVERT: e 186 MET cc_start: 0.8595 (pmm) cc_final: 0.8283 (pmm) REVERT: e 341 MET cc_start: 0.8172 (tpp) cc_final: 0.7786 (mmm) REVERT: e 390 MET cc_start: 0.7762 (pmm) cc_final: 0.7479 (pmm) REVERT: A 43 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7918 (tp) REVERT: U 137 ASN cc_start: 0.8304 (p0) cc_final: 0.8071 (p0) REVERT: W 30 MET cc_start: 0.8772 (tpp) cc_final: 0.8441 (mmm) REVERT: W 72 GLN cc_start: 0.9374 (tp-100) cc_final: 0.9036 (tp-100) REVERT: X 842 ASP cc_start: 0.7731 (t0) cc_final: 0.7412 (t0) REVERT: X 1230 MET cc_start: 0.7421 (tpp) cc_final: 0.7184 (tpp) REVERT: Y 151 MET cc_start: 0.8767 (ppp) cc_final: 0.8504 (ppp) REVERT: Y 180 MET cc_start: 0.4909 (tpt) cc_final: 0.3621 (tpt) REVERT: Y 466 MET cc_start: 0.7514 (tmm) cc_final: 0.6970 (tmm) REVERT: Y 513 MET cc_start: 0.8013 (mmm) cc_final: 0.7780 (mtt) REVERT: Y 704 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5721 (pm20) outliers start: 80 outliers final: 54 residues processed: 294 average time/residue: 0.5713 time to fit residues: 294.0238 Evaluate side-chains 271 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1056 VAL Chi-restraints excluded: chain X residue 1227 VAL Chi-restraints excluded: chain X residue 1287 LEU Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 242 LEU Chi-restraints excluded: chain Y residue 410 ASP Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 953 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.7980 chunk 584 optimal weight: 5.9990 chunk 533 optimal weight: 6.9990 chunk 568 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 446 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 513 optimal weight: 0.8980 chunk 537 optimal weight: 6.9990 chunk 566 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ** b 42 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** d 90 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 HIS ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 545 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 52482 Z= 0.170 Angle : 0.605 14.092 71218 Z= 0.294 Chirality : 0.041 0.366 8151 Planarity : 0.003 0.054 9004 Dihedral : 11.865 164.120 8012 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.19 % Allowed : 19.20 % Favored : 79.61 % 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: -0.28 (0.11), residues: 6306 helix: 0.97 (0.11), residues: 2328 sheet: -0.14 (0.18), residues: 801 loop : -1.08 (0.11), residues: 3177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 62 HIS 0.007 0.001 HIS c 295 PHE 0.028 0.001 PHE U 231 TYR 0.022 0.001 TYR X1229 ARG 0.006 0.000 ARG f 272 *********************** 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 284 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 220 time to evaluate : 6.585 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: f 21 MET cc_start: 0.6071 (mmm) cc_final: 0.5275 (mtt) REVERT: f 147 MET cc_start: 0.8317 (tpt) cc_final: 0.7619 (tpp) REVERT: f 416 MET cc_start: 0.9003 (mmm) cc_final: 0.8713 (mmm) REVERT: a 1 MET cc_start: 0.7847 (ppp) cc_final: 0.7224 (ppp) REVERT: a 147 MET cc_start: 0.8903 (tpt) cc_final: 0.8160 (tpp) REVERT: a 219 MET cc_start: 0.8583 (mmt) cc_final: 0.8319 (mmm) REVERT: a 396 MET cc_start: 0.8612 (mmm) cc_final: 0.7996 (mmm) REVERT: a 405 MET cc_start: 0.8123 (ptp) cc_final: 0.7920 (ppp) REVERT: b 1 MET cc_start: 0.8396 (ptm) cc_final: 0.8019 (ppp) REVERT: b 29 MET cc_start: 0.7055 (mpp) cc_final: 0.6163 (pmm) REVERT: b 147 MET cc_start: 0.8898 (tpp) cc_final: 0.7639 (tpp) REVERT: b 219 MET cc_start: 0.8228 (tpp) cc_final: 0.7836 (mmp) REVERT: b 405 MET cc_start: 0.9202 (ptp) cc_final: 0.8891 (ptp) REVERT: c 21 MET cc_start: 0.7192 (mtp) cc_final: 0.6432 (ptm) REVERT: c 205 MET cc_start: 0.7898 (mmm) cc_final: 0.7693 (mmm) REVERT: c 245 MET cc_start: 0.7227 (mmt) cc_final: 0.6937 (mmm) REVERT: c 390 MET cc_start: 0.6671 (ptt) cc_final: 0.5954 (ppp) REVERT: d 21 MET cc_start: 0.8460 (mmm) cc_final: 0.6376 (ptt) REVERT: d 245 MET cc_start: 0.8127 (tpp) cc_final: 0.7546 (mmt) REVERT: e 29 MET cc_start: 0.7229 (pmm) cc_final: 0.6781 (pmm) REVERT: e 186 MET cc_start: 0.8539 (pmm) cc_final: 0.8214 (pmm) REVERT: e 245 MET cc_start: 0.8722 (tmm) cc_final: 0.8245 (tmm) REVERT: e 390 MET cc_start: 0.7677 (pmm) cc_final: 0.7329 (pmm) REVERT: A 43 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7962 (tp) REVERT: U 137 ASN cc_start: 0.8279 (p0) cc_final: 0.8029 (p0) REVERT: W 30 MET cc_start: 0.8736 (tpp) cc_final: 0.8139 (mmp) REVERT: W 72 GLN cc_start: 0.9398 (tp-100) cc_final: 0.9066 (tp-100) REVERT: X 403 MET cc_start: 0.7912 (tmm) cc_final: 0.7627 (tmm) REVERT: X 842 ASP cc_start: 0.7754 (t0) cc_final: 0.7457 (t0) REVERT: X 1230 MET cc_start: 0.7358 (tpp) cc_final: 0.7079 (tpp) REVERT: Y 180 MET cc_start: 0.5138 (tpt) cc_final: 0.4704 (tpt) REVERT: Y 400 MET cc_start: 0.6302 (tmm) cc_final: 0.5106 (tpt) REVERT: Y 466 MET cc_start: 0.7465 (tmm) cc_final: 0.6751 (tmm) REVERT: Y 604 MET cc_start: 0.7961 (mmm) cc_final: 0.7550 (tpp) REVERT: Y 704 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5446 (pm20) REVERT: Y 708 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: Y 724 MET cc_start: 0.8471 (mpp) cc_final: 0.8257 (ptp) outliers start: 64 outliers final: 49 residues processed: 276 average time/residue: 0.6317 time to fit residues: 305.1537 Evaluate side-chains 269 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 326 LYS Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 194 GLN Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1056 VAL Chi-restraints excluded: chain X residue 1287 LEU Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 410 ASP Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 708 ASN Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 953 LYS Chi-restraints excluded: chain Y residue 1086 ASN 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: 8.9990 chunk 366 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 417 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 chunk 580 optimal weight: 8.9990 chunk 502 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 387 optimal weight: 0.0010 chunk 307 optimal weight: 0.0060 overall best weight: 1.1806 ------------------------------------------------------------------------------- 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 ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 344 HIS c 172 GLN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN Y 320 ASN ** Y 450 HIS ** 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: 0.7910 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 52482 Z= 0.152 Angle : 0.617 15.015 71218 Z= 0.295 Chirality : 0.041 0.331 8151 Planarity : 0.003 0.055 9004 Dihedral : 11.756 154.691 8012 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.96 % Allowed : 19.67 % Favored : 79.37 % 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: -0.22 (0.11), residues: 6306 helix: 1.00 (0.11), residues: 2329 sheet: -0.08 (0.18), residues: 827 loop : -1.04 (0.12), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 381 HIS 0.006 0.001 HIS c 295 PHE 0.013 0.001 PHE X 136 TYR 0.020 0.001 TYR X1229 ARG 0.008 0.000 ARG X 371 ********************** 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 271 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 5.915 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: f 21 MET cc_start: 0.5995 (mmm) cc_final: 0.5065 (mtt) REVERT: f 147 MET cc_start: 0.8225 (tpt) cc_final: 0.7515 (tpp) REVERT: f 341 MET cc_start: 0.8753 (tpp) cc_final: 0.8471 (tpt) REVERT: f 416 MET cc_start: 0.8984 (mmm) cc_final: 0.8694 (mmm) REVERT: a 1 MET cc_start: 0.7838 (ppp) cc_final: 0.7270 (ppp) REVERT: a 147 MET cc_start: 0.8902 (tpt) cc_final: 0.8203 (tpp) REVERT: a 219 MET cc_start: 0.8570 (mmt) cc_final: 0.8307 (mmm) REVERT: a 396 MET cc_start: 0.8583 (mmm) cc_final: 0.7977 (mmm) REVERT: b 1 MET cc_start: 0.8263 (ptm) cc_final: 0.7978 (ppp) REVERT: b 29 MET cc_start: 0.6978 (mpp) cc_final: 0.6091 (pmm) REVERT: b 147 MET cc_start: 0.8831 (tpp) cc_final: 0.7624 (tpp) REVERT: b 219 MET cc_start: 0.8210 (tpp) cc_final: 0.7861 (mmp) REVERT: c 21 MET cc_start: 0.7021 (mtp) cc_final: 0.6393 (ptm) REVERT: c 205 MET cc_start: 0.7930 (mmm) cc_final: 0.7535 (mmm) REVERT: c 245 MET cc_start: 0.7097 (mmt) cc_final: 0.6826 (mmm) REVERT: c 390 MET cc_start: 0.6600 (ptt) cc_final: 0.5711 (ppp) REVERT: d 21 MET cc_start: 0.8410 (mmm) cc_final: 0.6196 (ptt) REVERT: d 245 MET cc_start: 0.8096 (tpp) cc_final: 0.7521 (mmt) REVERT: e 21 MET cc_start: 0.7347 (ppp) cc_final: 0.7042 (ppp) REVERT: e 29 MET cc_start: 0.7298 (pmm) cc_final: 0.6837 (pmm) REVERT: e 186 MET cc_start: 0.8485 (pmm) cc_final: 0.8148 (pmm) REVERT: e 245 MET cc_start: 0.8745 (tmm) cc_final: 0.8257 (tmm) REVERT: e 390 MET cc_start: 0.7627 (pmm) cc_final: 0.7370 (pmm) REVERT: A 43 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (tp) REVERT: U 137 ASN cc_start: 0.8213 (p0) cc_final: 0.7991 (p0) REVERT: W 30 MET cc_start: 0.8701 (tpp) cc_final: 0.8120 (mmp) REVERT: W 72 GLN cc_start: 0.9391 (tp-100) cc_final: 0.9053 (tp-100) REVERT: X 403 MET cc_start: 0.7853 (tmm) cc_final: 0.7599 (tmm) REVERT: X 681 MET cc_start: 0.8054 (pmm) cc_final: 0.7749 (pmm) REVERT: X 842 ASP cc_start: 0.7647 (t0) cc_final: 0.7369 (t0) REVERT: X 1230 MET cc_start: 0.7300 (tpp) cc_final: 0.7030 (tpp) REVERT: Y 180 MET cc_start: 0.5020 (tpt) cc_final: 0.4622 (tpt) REVERT: Y 372 MET cc_start: 0.7976 (mmm) cc_final: 0.7760 (mmt) REVERT: Y 466 MET cc_start: 0.7466 (tmm) cc_final: 0.6790 (tmm) REVERT: Y 604 MET cc_start: 0.7944 (mmm) cc_final: 0.7520 (tpp) REVERT: Y 704 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: Y 708 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: Y 724 MET cc_start: 0.8533 (mpp) cc_final: 0.8172 (pmm) REVERT: Y 743 MET cc_start: 0.7664 (tmm) cc_final: 0.7175 (tmm) outliers start: 52 outliers final: 45 residues processed: 265 average time/residue: 0.6321 time to fit residues: 293.9150 Evaluate side-chains 264 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 5.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 230 SER Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 326 LYS Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 194 GLN Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 158 ASP Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1056 VAL Chi-restraints excluded: chain X residue 1227 VAL Chi-restraints excluded: chain Y residue 410 ASP Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 708 ASN Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 953 LYS Chi-restraints excluded: chain Y residue 974 VAL Chi-restraints excluded: chain Y residue 1086 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 3.9990 chunk 534 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 502 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 516 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN d 126 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN X1288 GLN ** Y 450 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.039418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.025496 restraints weight = 642076.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026062 restraints weight = 369579.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.026529 restraints weight = 256040.539| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52482 Z= 0.190 Angle : 0.626 15.569 71218 Z= 0.301 Chirality : 0.041 0.327 8151 Planarity : 0.003 0.053 9004 Dihedral : 11.778 148.924 8012 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.04 % Allowed : 19.70 % Favored : 79.26 % 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: -0.24 (0.11), residues: 6306 helix: 0.95 (0.11), residues: 2377 sheet: -0.07 (0.18), residues: 827 loop : -1.06 (0.12), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 381 HIS 0.006 0.001 HIS c 295 PHE 0.008 0.001 PHE a 355 TYR 0.021 0.001 TYR X1229 ARG 0.006 0.000 ARG Y 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8970.58 seconds wall clock time: 166 minutes 14.35 seconds (9974.35 seconds total)