Starting phenix.real_space_refine (version: dev) on Wed Dec 14 02:03:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/12_2022/7lpb_23475_neut_updated.pdb" } resolution = 3.54 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= 0.000 sd= 0.004 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 "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 636": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 636": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 709": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18392 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4403 Classifications: {'peptide': 596} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 124} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 580} Chain breaks: 5 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4403 Classifications: {'peptide': 596} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 124} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 580} Chain breaks: 5 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 Chain: "C" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4403 Classifications: {'peptide': 596} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 124} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 580} Chain breaks: 5 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 Chain: "D" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4403 Classifications: {'peptide': 596} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 124} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 580} Chain breaks: 5 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 15 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA D 204 " occ=0.50 Time building chain proxies: 10.91, per 1000 atoms: 0.59 Number of scatterers: 18392 At special positions: 0 Unit cell: (128.52, 128.52, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 16 15.00 O 3260 8.00 N 2900 7.00 C 12124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.05 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.05 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 2.8 seconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 8 sheets defined 58.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 127 through 138 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.902A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 429 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'A' and resid 469 through 498 Processing helix chain 'A' and resid 506 through 509 No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.727A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 596 removed outlier: 4.412A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 4.283A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 674 through 689 Processing helix chain 'A' and resid 692 through 716 removed outlier: 5.434A pdb=" N LYS A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 127 through 138 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.901A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'B' and resid 469 through 498 Processing helix chain 'B' and resid 506 through 509 No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 513 through 530 Processing helix chain 'B' and resid 535 through 557 removed outlier: 3.727A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 596 removed outlier: 4.412A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 4.283A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 Processing helix chain 'B' and resid 674 through 689 Processing helix chain 'B' and resid 692 through 716 removed outlier: 5.433A pdb=" N LYS B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 127 through 138 Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 204 through 211 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.902A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'C' and resid 469 through 498 Processing helix chain 'C' and resid 506 through 509 No H-bonds generated for 'chain 'C' and resid 506 through 509' Processing helix chain 'C' and resid 513 through 530 Processing helix chain 'C' and resid 535 through 557 removed outlier: 3.727A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 596 removed outlier: 4.411A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.283A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 669 Processing helix chain 'C' and resid 674 through 689 Processing helix chain 'C' and resid 692 through 716 removed outlier: 5.434A pdb=" N LYS C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS C 715 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET C 716 " --> pdb=" O PHE C 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 127 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.902A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 429 Processing helix chain 'D' and resid 431 through 452 Processing helix chain 'D' and resid 469 through 498 Processing helix chain 'D' and resid 506 through 509 No H-bonds generated for 'chain 'D' and resid 506 through 509' Processing helix chain 'D' and resid 513 through 530 Processing helix chain 'D' and resid 535 through 557 removed outlier: 3.728A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 596 removed outlier: 4.412A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 4.283A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 674 through 689 Processing helix chain 'D' and resid 692 through 716 removed outlier: 5.434A pdb=" N LYS D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS D 715 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET D 716 " --> pdb=" O PHE D 712 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.417A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 724 through 727 Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 6.416A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 724 through 727 Processing sheet with id= E, first strand: chain 'C' and resid 742 through 747 removed outlier: 6.416A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 724 through 727 Processing sheet with id= G, first strand: chain 'D' and resid 742 through 747 removed outlier: 6.416A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 724 through 727 972 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2796 1.30 - 1.43: 5179 1.43 - 1.56: 10421 1.56 - 1.69: 191 1.69 - 1.82: 173 Bond restraints: 18760 Sorted by residual: bond pdb=" O2 LBN A1000 " pdb=" P1 LBN A1000 " ideal model delta sigma weight residual 1.650 1.786 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" O2 LBN C1000 " pdb=" P1 LBN C1000 " ideal model delta sigma weight residual 1.650 1.786 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" O2 LBN D1000 " pdb=" P1 LBN D1000 " ideal model delta sigma weight residual 1.650 1.786 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" O2 LBN B1000 " pdb=" P1 LBN B1000 " ideal model delta sigma weight residual 1.650 1.786 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O22 6OU C1300 " pdb=" P23 6OU C1300 " ideal model delta sigma weight residual 1.643 1.767 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 18755 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.51: 236 105.51 - 112.63: 9571 112.63 - 119.76: 6523 119.76 - 126.89: 8894 126.89 - 134.02: 160 Bond angle restraints: 25384 Sorted by residual: angle pdb=" O1 LBN C1000 " pdb=" P1 LBN C1000 " pdb=" O2 LBN C1000 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O1 LBN D1000 " pdb=" P1 LBN D1000 " pdb=" O2 LBN D1000 " ideal model delta sigma weight residual 93.45 107.85 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O1 LBN A1000 " pdb=" P1 LBN A1000 " pdb=" O2 LBN A1000 " ideal model delta sigma weight residual 93.45 107.85 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O1 LBN B1000 " pdb=" P1 LBN B1000 " pdb=" O2 LBN B1000 " ideal model delta sigma weight residual 93.45 107.81 -14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O22 6OU B1300 " pdb=" P23 6OU B1300 " pdb=" O26 6OU B1300 " ideal model delta sigma weight residual 93.95 105.65 -11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 25379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 10452 31.96 - 63.91: 404 63.91 - 95.87: 32 95.87 - 127.82: 12 127.82 - 159.78: 12 Dihedral angle restraints: 10912 sinusoidal: 3900 harmonic: 7012 Sorted by residual: dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -44.27 -41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -44.29 -41.71 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual -86.00 -44.30 -41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 10909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2737 0.096 - 0.191: 135 0.191 - 0.287: 5 0.287 - 0.382: 7 0.382 - 0.478: 8 Chirality restraints: 2892 Sorted by residual: chirality pdb=" C2 LBN D1500 " pdb=" C1 LBN D1500 " pdb=" C3 LBN D1500 " pdb=" O7 LBN D1500 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" C2 LBN B1500 " pdb=" C1 LBN B1500 " pdb=" C3 LBN B1500 " pdb=" O7 LBN B1500 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2 LBN A1500 " pdb=" C1 LBN A1500 " pdb=" C3 LBN A1500 " pdb=" O7 LBN A1500 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2889 not shown) Planarity restraints: 3132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 251 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C PRO C 251 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO C 251 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 252 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 251 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C PRO A 251 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO A 251 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 252 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 251 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C PRO D 251 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO D 251 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 252 " -0.013 2.00e-02 2.50e+03 ... (remaining 3129 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3815 2.76 - 3.30: 18221 3.30 - 3.83: 28966 3.83 - 4.37: 32727 4.37 - 4.90: 57327 Nonbonded interactions: 141056 Sorted by model distance: nonbonded pdb=" O SER C 510 " pdb=" OG SER C 510 " model vdw 2.226 2.440 nonbonded pdb=" O SER D 510 " pdb=" OG SER D 510 " model vdw 2.226 2.440 nonbonded pdb=" O SER A 510 " pdb=" OG SER A 510 " model vdw 2.226 2.440 nonbonded pdb=" O SER B 510 " pdb=" OG SER B 510 " model vdw 2.226 2.440 nonbonded pdb=" O PHE C 517 " pdb=" OG SER C 520 " model vdw 2.238 2.440 ... (remaining 141051 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 C 12124 2.51 5 N 2900 2.21 5 O 3260 1.98 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=0.50 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.320 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 46.940 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.012 0.136 18760 Z= 0.790 Angle : 1.065 14.430 25384 Z= 0.528 Chirality : 0.055 0.478 2892 Planarity : 0.005 0.053 3132 Dihedral : 18.029 159.778 6372 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2336 helix: 0.22 (0.14), residues: 1432 sheet: -3.23 (0.52), residues: 84 loop : -2.48 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.140 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2625 time to fit residues: 124.4058 Evaluate side-chains 229 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.0040 chunk 184 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.0060 chunk 214 optimal weight: 1.9990 overall best weight: 0.8612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 498 GLN B 354 GLN B 498 GLN C 354 GLN C 498 GLN D 354 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 18760 Z= 0.159 Angle : 0.521 5.827 25384 Z= 0.272 Chirality : 0.038 0.136 2892 Planarity : 0.004 0.040 3132 Dihedral : 16.480 150.438 3000 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2336 helix: 1.25 (0.14), residues: 1444 sheet: -3.10 (0.50), residues: 84 loop : -2.05 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 1.964 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 296 average time/residue: 0.2620 time to fit residues: 123.1438 Evaluate side-chains 266 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1664 time to fit residues: 7.4061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 172 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 18760 Z= 0.276 Angle : 0.562 5.849 25384 Z= 0.293 Chirality : 0.040 0.130 2892 Planarity : 0.004 0.042 3132 Dihedral : 15.237 157.522 3000 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2336 helix: 1.08 (0.14), residues: 1456 sheet: -3.13 (0.49), residues: 84 loop : -1.78 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 2.213 Fit side-chains outliers start: 46 outliers final: 18 residues processed: 256 average time/residue: 0.2578 time to fit residues: 105.8079 Evaluate side-chains 249 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1571 time to fit residues: 8.1554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18760 Z= 0.141 Angle : 0.450 5.915 25384 Z= 0.238 Chirality : 0.036 0.119 2892 Planarity : 0.004 0.043 3132 Dihedral : 13.770 156.006 3000 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2336 helix: 1.53 (0.14), residues: 1448 sheet: -2.59 (0.52), residues: 84 loop : -1.65 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 2.029 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 275 average time/residue: 0.2562 time to fit residues: 113.2715 Evaluate side-chains 255 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2223 time to fit residues: 5.6885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18760 Z= 0.193 Angle : 0.479 6.137 25384 Z= 0.250 Chirality : 0.037 0.128 2892 Planarity : 0.004 0.043 3132 Dihedral : 13.743 160.600 3000 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2336 helix: 1.42 (0.14), residues: 1452 sheet: -2.51 (0.53), residues: 84 loop : -1.60 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 2.148 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 268 average time/residue: 0.2627 time to fit residues: 112.0821 Evaluate side-chains 248 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1975 time to fit residues: 7.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 228 optimal weight: 0.6980 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 18760 Z= 0.117 Angle : 0.422 6.376 25384 Z= 0.223 Chirality : 0.035 0.151 2892 Planarity : 0.004 0.044 3132 Dihedral : 12.799 156.947 3000 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2336 helix: 1.73 (0.14), residues: 1436 sheet: -2.51 (0.42), residues: 116 loop : -1.35 (0.22), residues: 784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 2.179 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 283 average time/residue: 0.2696 time to fit residues: 122.8224 Evaluate side-chains 257 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2268 time to fit residues: 5.3607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.0870 chunk 25 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 18760 Z= 0.127 Angle : 0.430 7.535 25384 Z= 0.226 Chirality : 0.036 0.151 2892 Planarity : 0.004 0.043 3132 Dihedral : 12.546 158.073 3000 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2336 helix: 1.73 (0.14), residues: 1452 sheet: -2.47 (0.40), residues: 116 loop : -1.39 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 2.172 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 255 average time/residue: 0.2775 time to fit residues: 112.8831 Evaluate side-chains 238 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1720 time to fit residues: 3.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 18760 Z= 0.226 Angle : 0.492 8.448 25384 Z= 0.257 Chirality : 0.038 0.140 2892 Planarity : 0.004 0.043 3132 Dihedral : 13.314 166.148 3000 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2336 helix: 1.54 (0.14), residues: 1456 sheet: -2.44 (0.50), residues: 84 loop : -1.32 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 2.084 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 247 average time/residue: 0.3032 time to fit residues: 120.7953 Evaluate side-chains 251 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1712 time to fit residues: 8.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 18760 Z= 0.145 Angle : 0.439 8.882 25384 Z= 0.233 Chirality : 0.036 0.162 2892 Planarity : 0.004 0.044 3132 Dihedral : 12.514 164.007 3000 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2336 helix: 1.75 (0.14), residues: 1436 sheet: -2.28 (0.50), residues: 84 loop : -1.31 (0.21), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 2.008 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.2664 time to fit residues: 104.0737 Evaluate side-chains 235 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 155 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 18760 Z= 0.128 Angle : 0.426 8.923 25384 Z= 0.224 Chirality : 0.035 0.168 2892 Planarity : 0.004 0.043 3132 Dihedral : 11.904 162.545 3000 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2336 helix: 1.92 (0.14), residues: 1428 sheet: -2.43 (0.38), residues: 116 loop : -1.17 (0.21), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 2.369 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 248 average time/residue: 0.2725 time to fit residues: 108.1811 Evaluate side-chains 247 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2052 time to fit residues: 4.5995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.228799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208785 restraints weight = 22965.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.205734 restraints weight = 42162.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.204521 restraints weight = 37852.174| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4516 r_free = 0.4516 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4514 r_free = 0.4514 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18760 Z= 0.143 Angle : 0.442 8.973 25384 Z= 0.232 Chirality : 0.036 0.164 2892 Planarity : 0.004 0.043 3132 Dihedral : 11.808 163.035 3000 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2336 helix: 1.88 (0.14), residues: 1432 sheet: -2.28 (0.39), residues: 116 loop : -1.15 (0.22), residues: 788 =============================================================================== Job complete usr+sys time: 2920.72 seconds wall clock time: 54 minutes 18.36 seconds (3258.36 seconds total)