Starting phenix.real_space_refine on Sun Mar 17 17:02:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_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_23475/03_2024/7lpb_23475_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpb_23475/03_2024/7lpb_23475_neut_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 130 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: 130 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: 130 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: 130 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: 10.02, per 1000 atoms: 0.54 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: 6.90 Conformation dependent library (CDL) restraints added in 3.6 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: 3.59 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: 5.31 Time building geometry restraints manager: 7.49 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: 10492 31.96 - 63.91: 456 63.91 - 95.87: 48 95.87 - 127.82: 36 127.82 - 159.78: 20 Dihedral angle restraints: 11052 sinusoidal: 4040 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 11049 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.280 Set scattering table: 0.200 Process input model: 48.650 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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= 0.789 Angle : 1.065 14.430 25384 Z= 0.528 Chirality : 0.055 0.478 2892 Planarity : 0.005 0.053 3132 Dihedral : 20.598 159.778 6512 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 740 HIS 0.006 0.001 HIS B 320 PHE 0.028 0.003 PHE D 559 TYR 0.035 0.003 TYR D 671 ARG 0.011 0.002 ARG C 557 *********************** 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 : 2.112 Fit side-chains REVERT: A 541 MET cc_start: 0.7566 (tmm) cc_final: 0.7340 (ttp) REVERT: A 636 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7755 (tp30) REVERT: B 399 ILE cc_start: 0.7942 (mt) cc_final: 0.7636 (mt) REVERT: B 541 MET cc_start: 0.7596 (tmm) cc_final: 0.7349 (ttp) REVERT: B 636 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7791 (tp30) REVERT: C 399 ILE cc_start: 0.7930 (mt) cc_final: 0.7626 (mt) REVERT: C 541 MET cc_start: 0.7606 (tmm) cc_final: 0.7349 (ttp) REVERT: C 636 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7766 (tp30) REVERT: D 365 LEU cc_start: 0.7990 (mm) cc_final: 0.7752 (tp) REVERT: D 541 MET cc_start: 0.7585 (tmm) cc_final: 0.7346 (ttp) REVERT: D 636 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7747 (tp30) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2628 time to fit residues: 124.2878 Evaluate side-chains 231 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6410 ------------------------------------------------------------------------------- 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: 0.7117 moved from start: 0.1603 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= 0.152 Angle : 0.535 7.193 25384 Z= 0.274 Chirality : 0.038 0.134 2892 Planarity : 0.004 0.040 3132 Dihedral : 19.042 163.882 3140 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.12 % Allowed : 6.82 % Favored : 92.06 % 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: 0.10 (0.18), residues: 2336 helix: 1.34 (0.14), residues: 1436 sheet: -3.07 (0.50), residues: 84 loop : -1.95 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.003 0.001 HIS D 364 PHE 0.034 0.001 PHE A 304 TYR 0.014 0.001 TYR D 199 ARG 0.004 0.001 ARG C 721 *********************** 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 324 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 1.890 Fit side-chains REVERT: A 743 ARG cc_start: 0.6639 (tmm160) cc_final: 0.5768 (ttm-80) REVERT: B 743 ARG cc_start: 0.6621 (tmm160) cc_final: 0.5734 (ttm-80) REVERT: C 427 ASP cc_start: 0.8127 (m-30) cc_final: 0.7900 (m-30) REVERT: C 743 ARG cc_start: 0.6561 (tmm160) cc_final: 0.5756 (ttm-80) REVERT: D 743 ARG cc_start: 0.6572 (tmm160) cc_final: 0.5736 (ttm-80) outliers start: 18 outliers final: 12 residues processed: 310 average time/residue: 0.2766 time to fit residues: 133.0415 Evaluate side-chains 282 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 270 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 599 ILE 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: 3.9990 chunk 59 optimal weight: 30.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 191 optimal weight: 0.0170 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN D 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18760 Z= 0.204 Angle : 0.502 5.711 25384 Z= 0.264 Chirality : 0.038 0.126 2892 Planarity : 0.004 0.043 3132 Dihedral : 17.326 164.135 3140 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.85 % Allowed : 10.61 % Favored : 86.54 % 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: 0.28 (0.17), residues: 2336 helix: 1.42 (0.14), residues: 1444 sheet: -2.92 (0.49), residues: 84 loop : -1.79 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 697 HIS 0.001 0.000 HIS D 320 PHE 0.030 0.002 PHE A 304 TYR 0.016 0.001 TYR A 199 ARG 0.004 0.001 ARG C 420 *********************** 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 301 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 1.841 Fit side-chains REVERT: A 509 ASP cc_start: 0.6387 (m-30) cc_final: 0.6168 (m-30) REVERT: A 743 ARG cc_start: 0.6658 (tmm160) cc_final: 0.5767 (ttm-80) REVERT: B 743 ARG cc_start: 0.6628 (tmm160) cc_final: 0.5764 (ttm-80) REVERT: C 743 ARG cc_start: 0.6648 (tmm160) cc_final: 0.5766 (ttm-80) REVERT: D 743 ARG cc_start: 0.6670 (tmm160) cc_final: 0.5780 (ttm-80) outliers start: 46 outliers final: 30 residues processed: 275 average time/residue: 0.2585 time to fit residues: 115.6923 Evaluate side-chains 270 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 741 CYS 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: 1.9990 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.2405 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= 0.143 Angle : 0.442 5.987 25384 Z= 0.235 Chirality : 0.036 0.117 2892 Planarity : 0.004 0.042 3132 Dihedral : 15.789 167.498 3140 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 12.34 % Favored : 85.73 % 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: 0.55 (0.18), residues: 2336 helix: 1.64 (0.14), residues: 1444 sheet: -2.74 (0.40), residues: 116 loop : -1.60 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 372 HIS 0.001 0.000 HIS B 378 PHE 0.029 0.001 PHE A 304 TYR 0.012 0.001 TYR D 199 ARG 0.003 0.000 ARG C 557 *********************** 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 301 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 2.093 Fit side-chains REVERT: B 427 ASP cc_start: 0.8204 (m-30) cc_final: 0.7994 (m-30) REVERT: B 743 ARG cc_start: 0.6646 (tmm160) cc_final: 0.5701 (ttm-80) REVERT: C 427 ASP cc_start: 0.8154 (m-30) cc_final: 0.7951 (m-30) REVERT: C 743 ARG cc_start: 0.6703 (tmm160) cc_final: 0.5783 (ttm-80) REVERT: D 743 ARG cc_start: 0.6573 (tmm160) cc_final: 0.5704 (ttm-80) outliers start: 31 outliers final: 15 residues processed: 284 average time/residue: 0.2690 time to fit residues: 124.2449 Evaluate side-chains 254 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 599 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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: 0.7212 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18760 Z= 0.233 Angle : 0.505 7.485 25384 Z= 0.262 Chirality : 0.038 0.121 2892 Planarity : 0.004 0.043 3132 Dihedral : 15.717 179.766 3140 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.23 % Allowed : 13.77 % Favored : 83.00 % 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: 0.42 (0.17), residues: 2336 helix: 1.44 (0.14), residues: 1444 sheet: -2.44 (0.54), residues: 84 loop : -1.58 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 372 HIS 0.001 0.000 HIS C 320 PHE 0.030 0.002 PHE A 304 TYR 0.015 0.001 TYR A 199 ARG 0.003 0.000 ARG B 557 *********************** 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 297 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 245 time to evaluate : 1.870 Fit side-chains REVERT: A 743 ARG cc_start: 0.6740 (tmm160) cc_final: 0.5672 (ttm-80) REVERT: B 743 ARG cc_start: 0.6708 (tmm160) cc_final: 0.5633 (ttm-80) REVERT: C 743 ARG cc_start: 0.6756 (tmm160) cc_final: 0.5693 (ttm-80) REVERT: D 743 ARG cc_start: 0.6707 (tmm160) cc_final: 0.5763 (ttm-80) outliers start: 52 outliers final: 33 residues processed: 276 average time/residue: 0.2553 time to fit residues: 113.1499 Evaluate side-chains 274 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 629 SER Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7170 moved from start: 0.2678 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= 0.154 Angle : 0.445 6.759 25384 Z= 0.234 Chirality : 0.036 0.139 2892 Planarity : 0.004 0.044 3132 Dihedral : 15.134 169.569 3140 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 15.51 % Favored : 82.57 % 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: 0.58 (0.18), residues: 2336 helix: 1.60 (0.14), residues: 1440 sheet: -2.26 (0.54), residues: 84 loop : -1.58 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 372 HIS 0.002 0.000 HIS A 378 PHE 0.029 0.001 PHE A 304 TYR 0.011 0.001 TYR B 199 ARG 0.003 0.000 ARG D 557 *********************** 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 281 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 1.910 Fit side-chains REVERT: A 743 ARG cc_start: 0.6695 (tmm160) cc_final: 0.5718 (ttm-80) REVERT: B 743 ARG cc_start: 0.6683 (tmm160) cc_final: 0.5695 (ttm-80) REVERT: C 743 ARG cc_start: 0.6707 (tmm160) cc_final: 0.5737 (ttm-80) REVERT: D 743 ARG cc_start: 0.6723 (tmm160) cc_final: 0.5746 (ttm-80) outliers start: 31 outliers final: 19 residues processed: 267 average time/residue: 0.2607 time to fit residues: 111.3526 Evaluate side-chains 259 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 741 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18760 Z= 0.208 Angle : 0.479 7.796 25384 Z= 0.251 Chirality : 0.037 0.123 2892 Planarity : 0.004 0.044 3132 Dihedral : 14.925 150.036 3140 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.67 % Allowed : 15.45 % Favored : 81.89 % 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: 0.52 (0.17), residues: 2336 helix: 1.46 (0.14), residues: 1452 sheet: -2.23 (0.53), residues: 84 loop : -1.45 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 697 HIS 0.003 0.000 HIS D 378 PHE 0.030 0.002 PHE A 304 TYR 0.013 0.001 TYR A 199 ARG 0.003 0.000 ARG B 557 *********************** 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 299 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 1.936 Fit side-chains REVERT: A 743 ARG cc_start: 0.6731 (tmm160) cc_final: 0.5694 (ttm-80) REVERT: B 743 ARG cc_start: 0.6703 (tmm160) cc_final: 0.5667 (ttm-80) REVERT: C 743 ARG cc_start: 0.6708 (tmm160) cc_final: 0.5651 (ttm-80) REVERT: D 743 ARG cc_start: 0.6723 (tmm160) cc_final: 0.5704 (ttm-80) outliers start: 43 outliers final: 36 residues processed: 280 average time/residue: 0.2565 time to fit residues: 115.8180 Evaluate side-chains 281 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 629 SER Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 741 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 154 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- 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: 0.7197 moved from start: 0.2876 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= 0.200 Angle : 0.465 7.693 25384 Z= 0.244 Chirality : 0.037 0.138 2892 Planarity : 0.004 0.044 3132 Dihedral : 14.475 151.701 3140 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.79 % Allowed : 15.45 % Favored : 81.76 % 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: 0.56 (0.17), residues: 2336 helix: 1.46 (0.14), residues: 1460 sheet: -2.29 (0.51), residues: 84 loop : -1.39 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 697 HIS 0.003 0.000 HIS C 378 PHE 0.029 0.001 PHE A 304 TYR 0.019 0.001 TYR D 495 ARG 0.003 0.000 ARG B 557 *********************** 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 286 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 1.939 Fit side-chains REVERT: A 743 ARG cc_start: 0.6749 (tmm160) cc_final: 0.5733 (ttm-80) REVERT: B 743 ARG cc_start: 0.6730 (tmm160) cc_final: 0.5729 (ttm-80) REVERT: C 743 ARG cc_start: 0.6752 (tmm160) cc_final: 0.5716 (ttm-80) REVERT: D 743 ARG cc_start: 0.6769 (tmm160) cc_final: 0.5731 (ttm-80) outliers start: 45 outliers final: 29 residues processed: 268 average time/residue: 0.2579 time to fit residues: 112.6422 Evaluate side-chains 271 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 741 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 285 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: 0.7138 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18760 Z= 0.122 Angle : 0.424 9.069 25384 Z= 0.222 Chirality : 0.035 0.165 2892 Planarity : 0.004 0.044 3132 Dihedral : 13.713 146.568 3140 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.62 % Allowed : 18.05 % Favored : 81.33 % 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: 0.93 (0.18), residues: 2336 helix: 1.84 (0.14), residues: 1428 sheet: -2.05 (0.52), residues: 84 loop : -1.31 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 372 HIS 0.003 0.000 HIS D 378 PHE 0.028 0.001 PHE A 304 TYR 0.015 0.001 TYR A 495 ARG 0.002 0.000 ARG A 420 *********************** 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 272 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 1.942 Fit side-chains REVERT: A 743 ARG cc_start: 0.6654 (tmm160) cc_final: 0.5847 (ttm-80) REVERT: B 743 ARG cc_start: 0.6633 (tmm160) cc_final: 0.5643 (ttm-80) REVERT: C 557 ARG cc_start: 0.8233 (ptp-170) cc_final: 0.8027 (ptp-170) REVERT: C 743 ARG cc_start: 0.6656 (tmm160) cc_final: 0.5636 (ttm-80) REVERT: D 743 ARG cc_start: 0.6644 (tmm160) cc_final: 0.5648 (ttm-80) outliers start: 10 outliers final: 9 residues processed: 264 average time/residue: 0.2546 time to fit residues: 106.8704 Evaluate side-chains 260 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain D residue 304 PHE 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: 0.9990 chunk 155 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.3192 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= 0.145 Angle : 0.435 6.151 25384 Z= 0.229 Chirality : 0.036 0.156 2892 Planarity : 0.004 0.044 3132 Dihedral : 13.497 146.257 3140 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.87 % Allowed : 18.05 % Favored : 81.08 % 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: 0.92 (0.18), residues: 2336 helix: 1.85 (0.14), residues: 1432 sheet: -2.30 (0.40), residues: 116 loop : -1.29 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 372 HIS 0.003 0.000 HIS D 378 PHE 0.029 0.001 PHE A 304 TYR 0.021 0.001 TYR D 495 ARG 0.002 0.000 ARG B 557 ********************** 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 263 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 1.929 Fit side-chains REVERT: A 743 ARG cc_start: 0.6849 (tmm160) cc_final: 0.5834 (ttm-80) REVERT: B 743 ARG cc_start: 0.6649 (tmm160) cc_final: 0.5695 (ttm-80) REVERT: C 743 ARG cc_start: 0.6678 (tmm160) cc_final: 0.5669 (ttm-80) REVERT: D 743 ARG cc_start: 0.6649 (tmm160) cc_final: 0.5648 (ttm-80) outliers start: 14 outliers final: 12 residues processed: 250 average time/residue: 0.2649 time to fit residues: 105.4560 Evaluate side-chains 255 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 0.0010 chunk 192 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.3808 ------------------------------------------------------------------------------- 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 285 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.228841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.187671 restraints weight = 22402.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183319 restraints weight = 32993.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179723 restraints weight = 29804.322| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18760 Z= 0.178 Angle : 0.461 6.762 25384 Z= 0.241 Chirality : 0.037 0.155 2892 Planarity : 0.004 0.043 3132 Dihedral : 13.572 148.880 3140 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.12 % Allowed : 18.05 % Favored : 80.83 % 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: 0.82 (0.18), residues: 2336 helix: 1.65 (0.14), residues: 1460 sheet: -2.12 (0.52), residues: 84 loop : -1.26 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 372 HIS 0.003 0.000 HIS D 378 PHE 0.029 0.001 PHE A 304 TYR 0.017 0.001 TYR A 495 ARG 0.003 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.81 seconds wall clock time: 59 minutes 8.80 seconds (3548.80 seconds total)