Starting phenix.real_space_refine (version: dev) on Tue Dec 13 01:56:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/12_2022/5irz_8118_trim_updated.pdb" } resolution = 3.28 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= 1.000 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 "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 474": "NH1" <-> "NH2" Residue "E ARG 491": "NH1" <-> "NH2" Residue "E ARG 557": "NH1" <-> "NH2" Residue "E TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12504 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 197 Chain: "E" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 197 Chain: "B" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 197 Chain: "C" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 197 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 7.68, per 1000 atoms: 0.61 Number of scatterers: 12504 At special positions: 0 Unit cell: (120.344, 120.344, 98.4636, 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 72 16.00 P 24 15.00 O 2196 8.00 N 1952 7.00 C 8260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 0 sheets defined 58.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 4.032A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 removed outlier: 3.776A pdb=" N ILE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 496 removed outlier: 3.628A pdb=" N PHE D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) 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 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.826A pdb=" N MET D 541 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 543 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 575 removed outlier: 3.593A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 598 removed outlier: 4.160A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 628 No H-bonds generated for 'chain 'D' and resid 603 through 628' Processing helix chain 'D' and resid 630 through 642 removed outlier: 3.891A pdb=" N GLU D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.545A pdb=" N LEU D 663 " --> pdb=" O PHE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 688 removed outlier: 3.813A pdb=" N ALA D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 709 removed outlier: 3.603A pdb=" N THR D 708 " --> pdb=" O THR D 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 416 through 428 removed outlier: 4.031A pdb=" N ARG E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 453 removed outlier: 3.776A pdb=" N ILE E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 496 removed outlier: 3.629A pdb=" N PHE E 496 " --> pdb=" O GLY E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 509 No H-bonds generated for 'chain 'E' and resid 506 through 509' Processing helix chain 'E' and resid 511 through 531 Processing helix chain 'E' and resid 535 through 556 removed outlier: 3.825A pdb=" N MET E 541 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 543 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E 546 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET E 547 " --> pdb=" O SER E 544 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP E 549 " --> pdb=" O ALA E 546 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 551 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 575 removed outlier: 3.593A pdb=" N TYR E 565 " --> pdb=" O GLN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 598 removed outlier: 4.160A pdb=" N PHE E 582 " --> pdb=" O CYS E 578 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 598 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 628 No H-bonds generated for 'chain 'E' and resid 603 through 628' Processing helix chain 'E' and resid 630 through 642 removed outlier: 3.890A pdb=" N GLU E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE E 640 " --> pdb=" O GLU E 636 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR E 641 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 670 removed outlier: 3.546A pdb=" N LEU E 663 " --> pdb=" O PHE E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 688 removed outlier: 3.814A pdb=" N ALA E 680 " --> pdb=" O ASN E 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN E 687 " --> pdb=" O GLY E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 709 removed outlier: 3.602A pdb=" N THR E 708 " --> pdb=" O THR E 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.032A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 removed outlier: 3.776A pdb=" N ILE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 496 removed outlier: 3.628A pdb=" N PHE B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) 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 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.826A pdb=" N MET B 541 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 removed outlier: 3.593A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 4.161A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 628 No H-bonds generated for 'chain 'B' and resid 603 through 628' Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.890A pdb=" N GLU B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.545A pdb=" N LEU B 663 " --> pdb=" O PHE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 688 removed outlier: 3.813A pdb=" N ALA B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 709 removed outlier: 3.603A pdb=" N THR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.033A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.777A pdb=" N ILE C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 496 removed outlier: 3.629A pdb=" N PHE C 496 " --> pdb=" O GLY C 492 " (cutoff:3.500A) 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 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.827A pdb=" N MET C 541 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.593A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 598 removed outlier: 4.160A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 628 No H-bonds generated for 'chain 'C' and resid 603 through 628' Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.890A pdb=" N GLU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.545A pdb=" N LEU C 663 " --> pdb=" O PHE C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 688 removed outlier: 3.813A pdb=" N ALA C 680 " --> pdb=" O ASN C 676 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 709 removed outlier: 3.602A pdb=" N THR C 708 " --> pdb=" O THR C 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1584 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: 3.16 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1792 1.29 - 1.42: 3648 1.42 - 1.55: 7144 1.55 - 1.68: 48 1.68 - 1.81: 124 Bond restraints: 12756 Sorted by residual: bond pdb=" C17 6O8 D 801 " pdb=" N18 6O8 D 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 B 801 " pdb=" N18 6O8 B 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 C 801 " pdb=" N18 6O8 C 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 E 801 " pdb=" N18 6O8 E 801 " ideal model delta sigma weight residual 1.506 1.423 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C19 6O8 C 801 " pdb=" N18 6O8 C 801 " ideal model delta sigma weight residual 1.490 1.411 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 12751 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.84: 203 105.84 - 112.88: 6714 112.88 - 119.93: 4842 119.93 - 126.97: 5405 126.97 - 134.02: 76 Bond angle restraints: 17240 Sorted by residual: angle pdb=" O04 6OE B 803 " pdb=" P05 6OE B 803 " pdb=" O08 6OE B 803 " ideal model delta sigma weight residual 93.39 110.06 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O04 6OE C 803 " pdb=" P05 6OE C 803 " pdb=" O08 6OE C 803 " ideal model delta sigma weight residual 93.39 110.03 -16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O04 6OE D 805 " pdb=" P05 6OE D 805 " pdb=" O08 6OE D 805 " ideal model delta sigma weight residual 93.39 110.00 -16.61 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O04 6OE E 804 " pdb=" P05 6OE E 804 " pdb=" O08 6OE E 804 " ideal model delta sigma weight residual 93.39 110.00 -16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O04 6OE B 805 " pdb=" P05 6OE B 805 " pdb=" O08 6OE B 805 " ideal model delta sigma weight residual 93.39 109.39 -16.00 3.00e+00 1.11e-01 2.84e+01 ... (remaining 17235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.65: 7069 28.65 - 57.30: 163 57.30 - 85.94: 28 85.94 - 114.59: 16 114.59 - 143.24: 20 Dihedral angle restraints: 7296 sinusoidal: 2684 harmonic: 4612 Sorted by residual: dihedral pdb=" CA GLY C 375 " pdb=" C GLY C 375 " pdb=" N PRO C 376 " pdb=" CA PRO C 376 " ideal model delta harmonic sigma weight residual -180.00 -139.32 -40.68 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" CA GLY E 375 " pdb=" C GLY E 375 " pdb=" N PRO E 376 " pdb=" CA PRO E 376 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA GLY D 375 " pdb=" C GLY D 375 " pdb=" N PRO D 376 " pdb=" CA PRO D 376 " ideal model delta harmonic sigma weight residual -180.00 -139.36 -40.64 0 5.00e+00 4.00e-02 6.61e+01 ... (remaining 7293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 1948 1.002 - 2.004: 0 2.004 - 3.006: 0 3.006 - 4.008: 0 4.008 - 5.010: 4 Chirality restraints: 1952 Sorted by residual: chirality pdb=" C16 6ES E 802 " pdb=" C17 6ES E 802 " pdb=" C21 6ES E 802 " pdb=" O15 6ES E 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C16 6ES D 802 " pdb=" C17 6ES D 802 " pdb=" C21 6ES D 802 " pdb=" O15 6ES D 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C16 6ES B 802 " pdb=" C17 6ES B 802 " pdb=" C21 6ES B 802 " pdb=" O15 6ES B 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.01 2.00e-01 2.50e+01 6.27e+02 ... (remaining 1949 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 375 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY E 375 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY E 375 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO E 376 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 375 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C GLY B 375 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY B 375 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 376 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 375 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C GLY D 375 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY D 375 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO D 376 " -0.012 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 137 2.59 - 3.16: 10228 3.16 - 3.74: 18547 3.74 - 4.32: 26134 4.32 - 4.90: 42253 Nonbonded interactions: 97299 Sorted by model distance: nonbonded pdb=" O ASP E 509 " pdb=" O22 6ES E 802 " model vdw 2.008 2.440 nonbonded pdb=" O ASP D 509 " pdb=" O22 6ES D 802 " model vdw 2.012 2.440 nonbonded pdb=" O ASP B 509 " pdb=" O22 6ES B 802 " model vdw 2.024 2.440 nonbonded pdb=" O ASP C 509 " pdb=" O22 6ES C 802 " model vdw 2.044 2.440 nonbonded pdb=" OE2 GLU C 570 " pdb=" O25 6ES C 802 " model vdw 2.175 2.440 ... (remaining 97294 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 24 5.49 5 S 72 5.16 5 C 8260 2.51 5 N 1952 2.21 5 O 2196 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.260 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: 2.960 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.110 Process input model: 34.550 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.010 0.084 12756 Z= 0.603 Angle : 1.308 16.665 17240 Z= 0.575 Chirality : 0.234 5.010 1952 Planarity : 0.005 0.048 2068 Dihedral : 16.219 143.240 4352 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -5.78 (0.14), residues: 1568 helix: -3.99 (0.08), residues: 960 sheet: -2.77 (0.66), residues: 56 loop : -3.24 (0.23), residues: 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2484 time to fit residues: 128.9282 Evaluate side-chains 229 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 410 HIS D 551 ASN ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 HIS E 551 ASN ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 551 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12756 Z= 0.210 Angle : 0.632 10.103 17240 Z= 0.321 Chirality : 0.043 0.266 1952 Planarity : 0.004 0.029 2068 Dihedral : 17.131 135.013 2052 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.82 (0.19), residues: 1568 helix: -1.27 (0.14), residues: 980 sheet: -2.44 (0.63), residues: 56 loop : -2.76 (0.27), residues: 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 285 average time/residue: 0.2101 time to fit residues: 89.0208 Evaluate side-chains 232 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1322 time to fit residues: 4.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.0270 chunk 153 optimal weight: 0.0370 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN C 561 GLN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12756 Z= 0.147 Angle : 0.562 11.808 17240 Z= 0.278 Chirality : 0.040 0.155 1952 Planarity : 0.003 0.053 2068 Dihedral : 15.665 146.395 2052 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.48 (0.20), residues: 1568 helix: 0.11 (0.16), residues: 960 sheet: -2.32 (0.60), residues: 56 loop : -2.80 (0.26), residues: 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 249 average time/residue: 0.2004 time to fit residues: 75.1648 Evaluate side-chains 220 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1207 time to fit residues: 3.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 551 ASN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 551 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12756 Z= 0.232 Angle : 0.569 9.039 17240 Z= 0.283 Chirality : 0.042 0.162 1952 Planarity : 0.003 0.034 2068 Dihedral : 14.734 139.129 2052 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.60 (0.22), residues: 1568 helix: 0.83 (0.16), residues: 972 sheet: -2.41 (0.56), residues: 56 loop : -2.50 (0.27), residues: 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 1.398 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 240 average time/residue: 0.1933 time to fit residues: 70.4768 Evaluate side-chains 229 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1076 time to fit residues: 5.5276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 551 ASN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12756 Z= 0.233 Angle : 0.554 7.114 17240 Z= 0.276 Chirality : 0.042 0.159 1952 Planarity : 0.003 0.035 2068 Dihedral : 14.289 140.311 2052 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.09 (0.22), residues: 1568 helix: 1.27 (0.17), residues: 956 sheet: -2.26 (0.57), residues: 56 loop : -2.27 (0.27), residues: 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.418 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 238 average time/residue: 0.2083 time to fit residues: 75.2095 Evaluate side-chains 246 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 225 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1221 time to fit residues: 6.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12756 Z= 0.171 Angle : 0.521 6.037 17240 Z= 0.262 Chirality : 0.041 0.140 1952 Planarity : 0.002 0.028 2068 Dihedral : 13.806 140.505 2052 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.21 (0.22), residues: 1568 helix: 1.54 (0.17), residues: 956 sheet: -1.98 (0.57), residues: 56 loop : -2.23 (0.27), residues: 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 1.709 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 251 average time/residue: 0.2017 time to fit residues: 77.2014 Evaluate side-chains 227 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 221 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1045 time to fit residues: 3.0226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 551 ASN C 628 ASN C 691 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12756 Z= 0.202 Angle : 0.526 6.278 17240 Z= 0.266 Chirality : 0.042 0.143 1952 Planarity : 0.002 0.025 2068 Dihedral : 13.607 140.870 2052 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.59 (0.22), residues: 1568 helix: 1.89 (0.17), residues: 928 sheet: -1.74 (0.60), residues: 56 loop : -1.99 (0.26), residues: 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.639 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 232 average time/residue: 0.2126 time to fit residues: 74.7435 Evaluate side-chains 230 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1359 time to fit residues: 4.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN E 551 ASN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 GLN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN C 691 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12756 Z= 0.189 Angle : 0.514 6.590 17240 Z= 0.261 Chirality : 0.042 0.153 1952 Planarity : 0.002 0.021 2068 Dihedral : 13.472 141.519 2052 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.67 (0.22), residues: 1568 helix: 1.93 (0.17), residues: 948 sheet: -1.77 (0.58), residues: 56 loop : -2.04 (0.27), residues: 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 2.043 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 234 average time/residue: 0.2145 time to fit residues: 76.4246 Evaluate side-chains 222 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1148 time to fit residues: 2.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 ASN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 551 ASN C 691 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12756 Z= 0.162 Angle : 0.509 7.323 17240 Z= 0.260 Chirality : 0.041 0.138 1952 Planarity : 0.002 0.020 2068 Dihedral : 13.287 141.339 2052 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.74 (0.22), residues: 1568 helix: 2.06 (0.17), residues: 932 sheet: -1.73 (0.57), residues: 56 loop : -2.05 (0.26), residues: 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.465 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 238 average time/residue: 0.2062 time to fit residues: 74.3640 Evaluate side-chains 230 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 222 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1217 time to fit residues: 3.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.0020 chunk 12 optimal weight: 0.0020 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN E 551 ASN E 628 ASN E 691 GLN B 551 ASN B 628 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 12756 Z= 0.130 Angle : 0.499 8.501 17240 Z= 0.253 Chirality : 0.040 0.139 1952 Planarity : 0.002 0.020 2068 Dihedral : 12.836 145.067 2052 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.72 (0.22), residues: 1568 helix: 2.05 (0.17), residues: 948 sheet: -1.42 (0.58), residues: 56 loop : -2.21 (0.26), residues: 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 242 time to evaluate : 1.293 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 247 average time/residue: 0.2112 time to fit residues: 78.4847 Evaluate side-chains 234 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1336 time to fit residues: 3.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN E 691 GLN B 628 ASN B 691 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090725 restraints weight = 22501.267| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.54 r_work: 0.2982 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12756 Z= 0.189 Angle : 0.520 9.033 17240 Z= 0.263 Chirality : 0.042 0.147 1952 Planarity : 0.002 0.021 2068 Dihedral : 12.852 138.192 2052 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.77 (0.22), residues: 1568 helix: 2.08 (0.17), residues: 948 sheet: -1.34 (0.59), residues: 56 loop : -2.19 (0.26), residues: 564 =============================================================================== Job complete usr+sys time: 2423.22 seconds wall clock time: 44 minutes 47.36 seconds (2687.36 seconds total)