Starting phenix.real_space_refine (version: dev) on Thu Dec 22 22:08:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/12_2022/7add_11724_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f GLU 351": "OE1" <-> "OE2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 125": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a GLU 351": "OE1" <-> "OE2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b GLU 351": "OE1" <-> "OE2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c GLU 351": "OE1" <-> "OE2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d GLU 351": "OE1" <-> "OE2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e GLU 108": "OE1" <-> "OE2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e GLU 351": "OE1" <-> "OE2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e ARG 384": "NH1" <-> "NH2" 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 GLU 367": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 181": "OE1" <-> "OE2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V GLU 136": "OE1" <-> "OE2" Residue "V GLU 165": "OE1" <-> "OE2" Residue "V GLU 204": "OE1" <-> "OE2" Residue "V GLU 261": "OE1" <-> "OE2" Residue "V ARG 265": "NH1" <-> "NH2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W GLU 74": "OE1" <-> "OE2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X GLU 244": "OE1" <-> "OE2" Residue "X ARG 268": "NH1" <-> "NH2" Residue "X GLU 308": "OE1" <-> "OE2" Residue "X ARG 371": "NH1" <-> "NH2" Residue "X ARG 451": "NH1" <-> "NH2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 565": "OE1" <-> "OE2" Residue "X ARG 647": "NH1" <-> "NH2" Residue "X GLU 705": "OE1" <-> "OE2" Residue "X GLU 825": "OE1" <-> "OE2" Residue "X ARG 903": "NH1" <-> "NH2" Residue "X GLU 940": "OE1" <-> "OE2" Residue "X GLU 950": "OE1" <-> "OE2" Residue "X GLU 963": "OE1" <-> "OE2" Residue "X ARG 996": "NH1" <-> "NH2" Residue "X GLU 1020": "OE1" <-> "OE2" Residue "X ARG 1034": "NH1" <-> "NH2" Residue "X ARG 1106": "NH1" <-> "NH2" Residue "X GLU 1137": "OE1" <-> "OE2" 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 ARG 314": "NH1" <-> "NH2" Residue "Y GLU 375": "OE1" <-> "OE2" Residue "Y GLU 386": "OE1" <-> "OE2" Residue "Y GLU 414": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ARG 515": "NH1" <-> "NH2" Residue "Y ARG 634": "NH1" <-> "NH2" Residue "Y ARG 692": "NH1" <-> "NH2" Residue "Y GLU 714": "OE1" <-> "OE2" Residue "Y GLU 827": "OE1" <-> "OE2" Residue "Y ARG 836": "NH1" <-> "NH2" Residue "Y GLU 866": "OE1" <-> "OE2" Residue "Y GLU 913": "OE1" <-> "OE2" Residue "Y ARG 933": "NH1" <-> "NH2" Residue "Y ARG 943": "NH1" <-> "NH2" Residue "Y ARG 1036": "NH1" <-> "NH2" Residue "Y GLU 1146": "OE1" <-> "OE2" 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 GLU 1254": "OE1" <-> "OE2" Residue "Y ARG 1258": "NH1" <-> "NH2" Residue "Y GLU 1327": "OE1" <-> "OE2" Residue "Y ARG 1345": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51610 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': 2, 'PTRANS': 54, '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: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "L" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 704 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "R" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 22} 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 54.748 119.874 118.065 1.00187.89 S ATOM 39518 SG CYS Y 72 54.953 116.532 119.073 1.00178.12 S ATOM 39626 SG CYS Y 85 52.811 118.016 121.591 1.00190.63 S ATOM 45338 SG CYS Y 814 69.868 185.845 119.810 1.00113.47 S ATOM 45903 SG CYS Y 888 72.009 181.687 119.875 1.00100.48 S ATOM 45954 SG CYS Y 895 68.988 181.850 118.048 1.00102.60 S ATOM 45975 SG CYS Y 898 72.521 184.573 117.833 1.00 95.45 S Time building chain proxies: 27.17, per 1000 atoms: 0.53 Number of scatterers: 51610 At special positions: 0 Unit cell: (162.44, 228.16, 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 98 15.00 Mg 6 11.99 F 15 9.00 O 10117 8.00 N 9121 7.00 C 32023 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.56 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " 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 895 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " 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: 224 helices and 47 sheets defined 35.7% alpha, 11.9% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 18.54 Creating SS restraints... Processing helix chain 'f' and resid 4 through 7 No H-bonds generated for 'chain 'f' and resid 4 through 7' Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 31 through 44 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 126 through 128 No H-bonds generated for 'chain 'f' and resid 126 through 128' Processing helix chain 'f' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU f 162 " --> 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 221 removed outlier: 3.916A pdb=" N ARG f 221 " --> pdb=" O THR f 217 " (cutoff:3.500A) 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: 4.274A 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 338 removed outlier: 4.683A pdb=" N GLY f 337 " --> pdb=" O GLU f 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR f 338 " --> pdb=" O GLU f 334 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 352 Processing helix chain 'f' and resid 368 through 371 Processing helix chain 'f' and resid 374 through 388 Processing helix chain 'f' and resid 393 through 404 Processing helix chain 'f' and resid 409 through 416 Processing helix chain 'a' and resid 4 through 7 No H-bonds generated for 'chain 'a' and resid 4 through 7' Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 31 through 44 Processing helix chain 'a' and resid 83 through 89 Processing helix chain 'a' and resid 126 through 128 No H-bonds generated for 'chain 'a' and resid 126 through 128' Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU a 162 " --> 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 221 removed outlier: 3.915A pdb=" N ARG a 221 " --> pdb=" O THR a 217 " (cutoff:3.500A) 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: 4.273A 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 338 removed outlier: 4.683A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR a 338 " --> pdb=" O GLU a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 352 Processing helix chain 'a' and resid 368 through 371 Processing helix chain 'a' and resid 374 through 388 Processing helix chain 'a' and resid 393 through 404 Processing helix chain 'a' and resid 409 through 416 Processing helix chain 'b' and resid 4 through 7 No H-bonds generated for 'chain 'b' and resid 4 through 7' Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 126 through 128 No H-bonds generated for 'chain 'b' and resid 126 through 128' Processing helix chain 'b' and resid 156 through 165 removed outlier: 3.645A pdb=" N LEU b 162 " --> 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 221 removed outlier: 3.916A pdb=" N ARG b 221 " --> pdb=" O THR b 217 " (cutoff:3.500A) 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: 4.274A 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 338 removed outlier: 4.683A pdb=" N GLY b 337 " --> pdb=" O GLU b 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR b 338 " --> pdb=" O GLU b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 352 Processing helix chain 'b' and resid 368 through 371 Processing helix chain 'b' and resid 374 through 388 Processing helix chain 'b' and resid 393 through 404 Processing helix chain 'b' and resid 409 through 416 Processing helix chain 'c' and resid 4 through 7 No H-bonds generated for 'chain 'c' and resid 4 through 7' Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 31 through 44 Processing helix chain 'c' and resid 83 through 89 Processing helix chain 'c' and resid 126 through 128 No H-bonds generated for 'chain 'c' and resid 126 through 128' Processing helix chain 'c' and resid 156 through 165 removed outlier: 3.645A pdb=" N LEU c 162 " --> 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 221 removed outlier: 3.915A pdb=" N ARG c 221 " --> pdb=" O THR c 217 " (cutoff:3.500A) 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: 4.273A 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 338 removed outlier: 4.682A pdb=" N GLY c 337 " --> pdb=" O GLU c 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR c 338 " --> pdb=" O GLU c 334 " (cutoff:3.500A) Processing helix chain 'c' and resid 347 through 352 Processing helix chain 'c' and resid 368 through 371 Processing helix chain 'c' and resid 374 through 388 Processing helix chain 'c' and resid 393 through 404 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'd' and resid 4 through 7 No H-bonds generated for 'chain 'd' and resid 4 through 7' Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 31 through 44 Processing helix chain 'd' and resid 83 through 89 Processing helix chain 'd' and resid 126 through 128 No H-bonds generated for 'chain 'd' and resid 126 through 128' Processing helix chain 'd' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU d 162 " --> 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 221 removed outlier: 3.915A pdb=" N ARG d 221 " --> pdb=" O THR d 217 " (cutoff:3.500A) 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: 4.273A 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 338 removed outlier: 4.683A pdb=" N GLY d 337 " --> pdb=" O GLU d 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 352 Processing helix chain 'd' and resid 368 through 371 Processing helix chain 'd' and resid 374 through 388 Processing helix chain 'd' and resid 393 through 404 Processing helix chain 'd' and resid 409 through 416 Processing helix chain 'e' and resid 4 through 7 No H-bonds generated for 'chain 'e' and resid 4 through 7' Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 31 through 44 Processing helix chain 'e' and resid 83 through 89 Processing helix chain 'e' and resid 126 through 128 No H-bonds generated for 'chain 'e' and resid 126 through 128' Processing helix chain 'e' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU e 162 " --> 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 221 removed outlier: 3.914A pdb=" N ARG e 221 " --> pdb=" O THR e 217 " (cutoff:3.500A) 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: 4.273A 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 338 removed outlier: 4.683A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 352 Processing helix chain 'e' and resid 368 through 371 Processing helix chain 'e' and resid 374 through 388 Processing helix chain 'e' and resid 393 through 404 Processing helix chain 'e' and resid 409 through 416 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 130 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 258 through 266 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 332 removed outlier: 6.294A pdb=" N ASN A 324 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 327 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 424 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 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' 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 164 through 166 No H-bonds generated for 'chain 'U' and resid 164 through 166' Processing helix chain 'U' and resid 213 through 230 removed outlier: 3.853A pdb=" N ALA U 230 " --> pdb=" O GLU U 226 " (cutoff:3.500A) 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 165 removed outlier: 4.308A pdb=" N GLU V 165 " --> pdb=" O SER V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 231 removed outlier: 4.797A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.534A 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 273 removed outlier: 3.793A pdb=" N GLU V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 281 No H-bonds generated for 'chain 'V' and resid 278 through 281' 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 297 through 308 removed outlier: 4.363A pdb=" N LEU V 307 " --> pdb=" O ILE V 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA V 308 " --> pdb=" O LYS V 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 10 No H-bonds generated for 'chain 'W' and resid 7 through 10' Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 46 through 56 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 36 Processing helix chain 'X' and resid 43 through 45 No H-bonds generated for 'chain 'X' and resid 43 through 45' Processing helix chain 'X' and resid 50 through 54 Processing helix chain 'X' and resid 82 through 88 Processing helix chain 'X' and resid 206 through 213 removed outlier: 4.022A 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 280 removed outlier: 3.616A pdb=" N ASP X 280 " --> pdb=" O GLN X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 289 through 294 removed outlier: 3.847A pdb=" N GLY X 294 " --> pdb=" O GLU X 290 " (cutoff:3.500A) 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 380 through 389 removed outlier: 3.720A 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 479 removed outlier: 3.753A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 498 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 665 through 667 No H-bonds generated for 'chain 'X' and resid 665 through 667' Processing helix chain 'X' and resid 676 through 688 removed outlier: 3.622A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN X 688 " --> pdb=" O ASN X 684 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 711 removed outlier: 3.923A pdb=" N VAL X 708 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA X 709 " --> pdb=" O ARG X 706 " (cutoff:3.500A) removed outlier: 3.882A 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 859 through 864 removed outlier: 4.174A pdb=" N LYS X 864 " --> pdb=" O ALA X 860 " (cutoff:3.500A) Processing helix chain 'X' and resid 897 through 903 Processing helix chain 'X' and resid 943 through 979 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: 5.280A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1082 through 1084 No H-bonds generated for 'chain 'X' and resid 1082 through 1084' Processing helix chain 'X' and resid 1102 through 1105 No H-bonds generated for 'chain 'X' and resid 1102 through 1105' Processing helix chain 'X' and resid 1110 through 1132 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 1272 through 1280 Processing helix chain 'X' and resid 1284 through 1291 Processing helix chain 'X' and resid 1298 through 1308 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 123 through 127 Processing helix chain 'Y' and resid 132 through 139 Processing helix chain 'Y' and resid 162 through 166 Processing helix chain 'Y' and resid 182 through 191 removed outlier: 3.770A pdb=" N SER Y 191 " --> pdb=" O ALA Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 207 Processing helix chain 'Y' and resid 212 through 229 removed outlier: 3.502A pdb=" N ALA Y 226 " --> pdb=" O LYS Y 222 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Y 227 " --> pdb=" O LEU Y 223 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 237 Processing helix chain 'Y' and resid 264 through 284 removed outlier: 3.843A pdb=" N ASP Y 284 " --> pdb=" O LYS Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 289 through 307 removed outlier: 4.370A pdb=" N ARG Y 293 " --> pdb=" O ASP Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 331 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 453 through 457 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 539 Processing helix chain 'Y' and resid 574 through 581 removed outlier: 4.084A 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: 4.470A 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 701 removed outlier: 3.838A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE Y 685 " --> pdb=" O LYS Y 681 " (cutoff:3.500A) 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: 3.978A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.892A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.369A 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: 4.939A pdb=" N GLN Y 929 " --> pdb=" O GLU Y 925 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1069 through 1072 No H-bonds generated for 'chain 'Y' and resid 1069 through 1072' Processing helix chain 'Y' and resid 1138 through 1146 Processing helix chain 'Y' and resid 1217 through 1224 Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.711A 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 removed outlier: 4.151A pdb=" N GLU Y1291 " --> pdb=" O ILE Y1287 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Y1292 " --> pdb=" O ALA Y1288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y1294 " --> pdb=" O ARG Y1290 " (cutoff:3.500A) 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 1323 Processing helix chain 'Y' and resid 1328 through 1338 Processing helix chain 'Y' and resid 1348 through 1352 Processing helix chain 'Y' and resid 1361 through 1372 removed outlier: 4.017A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'f' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.824A 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 345 removed outlier: 7.621A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP f 265 " --> pdb=" O MET f 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU f 207 " --> pdb=" O ASP f 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP f 210 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER f 230 " --> pdb=" O ASP f 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 79 through 81 removed outlier: 3.704A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.824A 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 345 removed outlier: 7.622A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP a 265 " --> pdb=" O MET a 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU a 207 " --> pdb=" O ASP a 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP a 210 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER a 230 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.825A 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 345 removed outlier: 7.621A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP b 265 " --> pdb=" O MET b 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU b 207 " --> pdb=" O ASP b 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP b 210 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER b 230 " --> pdb=" O ASP b 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 79 through 81 removed outlier: 3.706A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.825A 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 345 removed outlier: 7.621A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP c 265 " --> pdb=" O MET c 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU c 207 " --> pdb=" O ASP c 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP c 210 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER c 230 " --> pdb=" O ASP c 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'd' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.825A 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 345 removed outlier: 7.621A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP d 265 " --> pdb=" O MET d 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU d 207 " --> pdb=" O ASP d 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP d 210 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER d 230 " --> pdb=" O ASP d 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'e' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.824A 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 345 removed outlier: 7.621A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP e 265 " --> pdb=" O MET e 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU e 207 " --> pdb=" O ASP e 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP e 210 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER e 230 " --> pdb=" O ASP e 210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.909A pdb=" N LYS A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 142 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 270 through 275 Processing sheet with id= O, first strand: chain 'A' and resid 297 through 299 removed outlier: 6.452A pdb=" N GLU A 335 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 24 through 28 Processing sheet with id= Q, first strand: chain 'U' and resid 170 through 172 removed outlier: 6.862A pdb=" N LYS U 145 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL U 59 " --> pdb=" O ARG U 143 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG U 143 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE U 61 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER U 141 " --> pdb=" O ILE U 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 90 through 92 Processing sheet with id= S, first strand: chain 'U' and resid 108 through 111 Processing sheet with id= T, first strand: chain 'V' and resid 23 through 28 Processing sheet with id= U, first strand: chain 'V' and resid 90 through 92 Processing sheet with id= V, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.177A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 93 through 95 Processing sheet with id= X, first strand: chain 'X' and resid 118 through 123 removed outlier: 3.964A pdb=" N SER X 72 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG X 101 " --> pdb=" O TYR X 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR X 70 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL X 103 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU X 68 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 143 through 145 Processing sheet with id= Z, first strand: chain 'X' and resid 148 through 151 Processing sheet with id= AA, first strand: chain 'X' and resid 154 through 160 removed outlier: 6.381A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 228 through 231 Processing sheet with id= AC, first strand: chain 'X' and resid 603 through 606 Processing sheet with id= AD, first strand: chain 'X' and resid 634 through 637 Processing sheet with id= AE, first strand: chain 'X' and resid 748 through 752 removed outlier: 6.463A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'X' and resid 1227 through 1232 removed outlier: 6.667A pdb=" N ILE X1096 " --> pdb=" O ALA X 803 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 830 through 839 removed outlier: 3.752A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 1065 through 1067 Processing sheet with id= AI, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.446A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AK, first strand: chain 'Y' and resid 145 through 147 removed outlier: 4.166A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Y' and resid 350 through 354 Processing sheet with id= AM, first strand: chain 'Y' and resid 355 through 358 removed outlier: 5.956A pdb=" N ILE Y 447 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY Y 358 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU Y 449 " --> pdb=" O GLY Y 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'Y' and resid 365 through 369 removed outlier: 5.747A pdb=" N GLU Y 438 " --> pdb=" O CYS Y 366 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU Y 368 " --> pdb=" O GLU Y 438 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL Y 440 " --> pdb=" O LEU Y 368 " (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: 3.548A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 3.870A 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 1113 through 1115 removed outlier: 4.077A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG Y1036 " --> pdb=" O LYS Y1079 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Y1079 " --> pdb=" O ARG Y1036 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Y' and resid 1162 through 1165 removed outlier: 3.749A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Y' and resid 1264 through 1266 1680 hydrogen bonds defined for protein. 4788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 21.47 Time building geometry restraints manager: 22.25 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: 16779 1.34 - 1.45: 6153 1.45 - 1.57: 29006 1.57 - 1.69: 186 1.69 - 1.81: 408 Bond restraints: 52532 Sorted by residual: bond pdb=" BE BEF a1002 " pdb=" F2 BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" BE BEF c 504 " pdb=" F2 BEF c 504 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" BE BEF c 503 " pdb=" F2 BEF c 503 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 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 e1002 " pdb=" F2 BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 52527 not shown) Histogram of bond angle deviations from ideal: 82.25 - 93.01: 2 93.01 - 103.77: 912 103.77 - 114.52: 32781 114.52 - 125.28: 36854 125.28 - 136.04: 745 Bond angle restraints: 71294 Sorted by residual: angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP2 DC L 21 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP1 DC L 21 " ideal model delta sigma weight residual 108.00 84.32 23.68 3.00e+00 1.11e-01 6.23e+01 angle pdb=" CB LYS e 326 " pdb=" CG LYS e 326 " pdb=" CD LYS e 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS b 326 " pdb=" CG LYS b 326 " pdb=" CD LYS b 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS c 326 " pdb=" CG LYS c 326 " pdb=" CD LYS c 326 " ideal model delta sigma weight residual 111.30 122.87 -11.57 2.30e+00 1.89e-01 2.53e+01 ... (remaining 71289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 31308 35.23 - 70.46: 763 70.46 - 105.68: 52 105.68 - 140.91: 5 140.91 - 176.14: 7 Dihedral angle restraints: 32135 sinusoidal: 13937 harmonic: 18198 Sorted by residual: dihedral pdb=" O4' U R 24 " pdb=" C1' U R 24 " pdb=" N1 U R 24 " pdb=" C2 U R 24 " ideal model delta sinusoidal sigma weight residual 232.00 62.28 169.72 1 1.70e+01 3.46e-03 6.59e+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 -60.00 102.99 -163.00 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP c 501 " pdb=" O5' ADP c 501 " pdb=" PA ADP c 501 " pdb=" O2A ADP c 501 " ideal model delta sinusoidal sigma weight residual 300.00 153.86 146.14 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 32132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 8159 0.401 - 0.802: 0 0.802 - 1.203: 0 1.203 - 1.604: 0 1.604 - 2.005: 1 Chirality restraints: 8160 Sorted by residual: chirality pdb=" P DC L 21 " pdb=" OP1 DC L 21 " pdb=" OP2 DC L 21 " pdb=" O5' DC L 21 " both_signs ideal model delta sigma weight residual True 2.35 0.34 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" P DC K -14 " pdb=" OP1 DC K -14 " pdb=" OP2 DC K -14 " pdb=" O5' DC K -14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.45e-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 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 8157 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG L 2 " -0.026 2.00e-02 2.50e+03 1.26e-02 4.74e+00 pdb=" N9 DG L 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG L 2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG L 2 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG L 2 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG L 2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 658 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C GLU Y 658 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU Y 658 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Y 659 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU U 29 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO U 30 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO U 30 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO U 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 650 2.57 - 3.16: 42853 3.16 - 3.74: 84005 3.74 - 4.32: 111574 4.32 - 4.90: 177813 Nonbonded interactions: 416895 Sorted by model distance: nonbonded pdb="MG MG c 502 " pdb=" F3 BEF c 503 " model vdw 1.993 2.120 nonbonded pdb=" O1B ADP c 501 " pdb="MG MG c 502 " model vdw 2.008 2.170 nonbonded pdb=" O1B ADP d1000 " pdb="MG MG d1001 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP b1000 " pdb="MG MG b1001 " model vdw 2.034 2.170 nonbonded pdb=" F3 BEF c 504 " pdb="MG MG d1001 " model vdw 2.046 2.120 ... (remaining 416890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 98 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 32023 2.51 5 N 9121 2.21 5 O 10117 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.750 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.390 Process input model: 142.500 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.087 52532 Z= 0.160 Angle : 0.583 25.746 71294 Z= 0.311 Chirality : 0.046 2.005 8160 Planarity : 0.003 0.042 9006 Dihedral : 15.188 176.142 20389 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -2.89 (0.09), residues: 6306 helix: -1.25 (0.10), residues: 2388 sheet: -1.55 (0.15), residues: 803 loop : -2.57 (0.10), residues: 3115 *********************** 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 565 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 379 time to evaluate : 5.545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 48 residues processed: 546 average time/residue: 0.6907 time to fit residues: 616.4207 Evaluate side-chains 305 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 257 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4610 time to fit residues: 49.4555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 9.9990 chunk 479 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 323 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 496 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 369 optimal weight: 0.8980 chunk 574 optimal weight: 0.3980 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 2 ASN f 90 ASN f 172 GLN f 361 ASN a 90 ASN a 172 GLN a 361 ASN b 2 ASN b 41 GLN b 90 ASN b 172 GLN b 361 ASN c 41 GLN c 90 ASN c 117 ASN c 172 GLN c 361 ASN d 90 ASN d 117 ASN d 172 GLN d 361 ASN e 90 ASN e 117 ASN e 172 GLN e 361 ASN A 14 ASN A 157 ASN A 172 ASN A 282 GLN A 324 ASN A 330 GLN V 147 GLN V 239 GLN V 276 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 343 HIS ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 580 GLN X 618 GLN X 808 ASN X 932 GLN X1009 ASN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1017 GLN X1209 GLN X1312 ASN Y 80 HIS Y 196 GLN Y 266 ASN Y 277 ASN Y 341 ASN Y 365 GLN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 545 HIS Y 702 GLN Y 865 HIS Y1023 HIS ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 52532 Z= 0.192 Angle : 0.559 25.715 71294 Z= 0.276 Chirality : 0.046 2.006 8160 Planarity : 0.003 0.056 9006 Dihedral : 11.745 177.426 7879 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -1.88 (0.10), residues: 6306 helix: -0.21 (0.11), residues: 2392 sheet: -1.28 (0.15), residues: 886 loop : -2.10 (0.10), residues: 3028 *********************** 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 284 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 280 time to evaluate : 6.338 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 outliers start: 4 outliers final: 1 residues processed: 284 average time/residue: 0.6909 time to fit residues: 324.4556 Evaluate side-chains 245 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 6.063 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4958 time to fit residues: 9.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 478 optimal weight: 0.6980 chunk 391 optimal weight: 20.0000 chunk 158 optimal weight: 0.0060 chunk 575 optimal weight: 0.8980 chunk 622 optimal weight: 5.9990 chunk 512 optimal weight: 8.9990 chunk 571 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 overall best weight: 3.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS e 41 GLN A 129 GLN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1013 GLN X1209 GLN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1084 GLN ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1350 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 52532 Z= 0.177 Angle : 0.544 25.913 71294 Z= 0.268 Chirality : 0.045 2.002 8160 Planarity : 0.003 0.072 9006 Dihedral : 11.741 177.330 7879 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -1.42 (0.10), residues: 6306 helix: 0.18 (0.11), residues: 2391 sheet: -0.99 (0.16), residues: 878 loop : -1.86 (0.11), residues: 3037 *********************** 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 268 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 6.031 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 outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.6761 time to fit residues: 299.6778 Evaluate side-chains 236 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 5.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 2.9990 chunk 432 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 386 optimal weight: 9.9990 chunk 577 optimal weight: 20.0000 chunk 611 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 547 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 2 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 135 ASN c 2 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1116 HIS Y 232 ASN Y 320 ASN ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 52532 Z= 0.297 Angle : 0.644 26.160 71294 Z= 0.323 Chirality : 0.046 2.000 8160 Planarity : 0.004 0.053 9006 Dihedral : 11.896 177.460 7879 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -1.13 (0.10), residues: 6306 helix: 0.35 (0.11), residues: 2393 sheet: -0.98 (0.17), residues: 855 loop : -1.56 (0.11), residues: 3058 *********************** 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 263 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 5.977 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 outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.6999 time to fit residues: 308.2503 Evaluate side-chains 229 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 6.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 0.9990 chunk 347 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 522 optimal weight: 9.9990 chunk 422 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 549 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 613 ASN ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 52532 Z= 0.193 Angle : 0.565 26.281 71294 Z= 0.281 Chirality : 0.046 2.000 8160 Planarity : 0.004 0.054 9006 Dihedral : 11.790 178.136 7879 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.93 (0.10), residues: 6306 helix: 0.50 (0.11), residues: 2404 sheet: -0.85 (0.17), residues: 882 loop : -1.45 (0.11), residues: 3020 *********************** 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 261 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 6.106 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 outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.6564 time to fit residues: 290.3845 Evaluate side-chains 227 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 5.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 20.0000 chunk 551 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 612 optimal weight: 0.9990 chunk 508 optimal weight: 0.6980 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 52532 Z= 0.144 Angle : 0.543 26.304 71294 Z= 0.267 Chirality : 0.046 1.995 8160 Planarity : 0.004 0.200 9006 Dihedral : 11.611 178.336 7879 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.75 (0.11), residues: 6306 helix: 0.65 (0.11), residues: 2392 sheet: -0.70 (0.17), residues: 872 loop : -1.37 (0.11), residues: 3042 *********************** 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 259 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 5.901 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 outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.6719 time to fit residues: 293.8181 Evaluate side-chains 228 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 6.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 348 optimal weight: 20.0000 chunk 447 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 chunk 515 optimal weight: 50.0000 chunk 341 optimal weight: 40.0000 chunk 610 optimal weight: 4.9990 chunk 381 optimal weight: 6.9990 chunk 371 optimal weight: 20.0000 chunk 281 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 190 ASN f 198 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 2 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 HIS ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 618 GLN ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1295 ASN ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 52532 Z= 0.324 Angle : 0.687 26.437 71294 Z= 0.347 Chirality : 0.047 2.001 8160 Planarity : 0.005 0.140 9006 Dihedral : 11.887 177.622 7879 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.85 (0.10), residues: 6306 helix: 0.51 (0.11), residues: 2395 sheet: -0.87 (0.17), residues: 866 loop : -1.32 (0.11), residues: 3045 *********************** 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 244 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 5.807 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 outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.6486 time to fit residues: 268.9375 Evaluate side-chains 217 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 5.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 364 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 387 optimal weight: 0.8980 chunk 415 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 479 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN U 132 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 52532 Z= 0.197 Angle : 0.588 26.492 71294 Z= 0.294 Chirality : 0.046 1.994 8160 Planarity : 0.004 0.105 9006 Dihedral : 11.818 179.715 7879 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.67 (0.11), residues: 6306 helix: 0.70 (0.11), residues: 2387 sheet: -0.94 (0.17), residues: 874 loop : -1.19 (0.11), residues: 3045 *********************** 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 240 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 5.601 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 outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.6350 time to fit residues: 262.3718 Evaluate side-chains 221 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 5.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 4.9990 chunk 584 optimal weight: 20.0000 chunk 533 optimal weight: 5.9990 chunk 568 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 174 optimal weight: 0.0070 chunk 513 optimal weight: 20.0000 chunk 537 optimal weight: 30.0000 chunk 566 optimal weight: 6.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 85 GLN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 ASN e 275 ASN V 23 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1209 GLN X1268 GLN ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 52532 Z= 0.240 Angle : 0.618 26.364 71294 Z= 0.309 Chirality : 0.046 1.994 8160 Planarity : 0.004 0.089 9006 Dihedral : 11.818 178.794 7879 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.63 (0.11), residues: 6306 helix: 0.69 (0.11), residues: 2402 sheet: -0.90 (0.17), residues: 871 loop : -1.14 (0.11), residues: 3033 *********************** 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 234 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 7.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.6237 time to fit residues: 251.2367 Evaluate side-chains 215 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 5.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 6.9990 chunk 601 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 417 optimal weight: 3.9990 chunk 630 optimal weight: 10.0000 chunk 580 optimal weight: 5.9990 chunk 502 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 126 ASN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN e 275 ASN A 436 ASN ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1008 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1135 GLN ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 739 GLN ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 52532 Z= 0.279 Angle : 0.656 26.370 71294 Z= 0.332 Chirality : 0.047 1.986 8160 Planarity : 0.004 0.086 9006 Dihedral : 11.931 179.643 7879 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 27.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.71 (0.11), residues: 6306 helix: 0.60 (0.11), residues: 2404 sheet: -1.05 (0.17), residues: 802 loop : -1.14 (0.11), residues: 3100 ********************** 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 234 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 6.023 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 outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.6371 time to fit residues: 253.2799 Evaluate side-chains 219 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 5.956 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 0.7980 chunk 534 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 463 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 502 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 516 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.033192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.020695 restraints weight = 795289.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.020966 restraints weight = 577341.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.021212 restraints weight = 459891.328| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 52532 Z= 0.209 Angle : 0.609 26.370 71294 Z= 0.303 Chirality : 0.047 1.980 8160 Planarity : 0.004 0.064 9006 Dihedral : 11.838 179.370 7879 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % 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: -0.56 (0.11), residues: 6306 helix: 0.71 (0.11), residues: 2395 sheet: -0.91 (0.17), residues: 846 loop : -1.05 (0.11), residues: 3065 =============================================================================== Job complete usr+sys time: 8067.57 seconds wall clock time: 148 minutes 22.94 seconds (8902.94 seconds total)