Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:39:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_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_8118/02_2023/5irz_8118_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_8118_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/02_2023/5irz_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 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-4877/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: 7.50, per 1000 atoms: 0.60 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: 5.21 Conformation dependent library (CDL) restraints added in 1.8 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: 1.00 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: 3.35 Time building geometry restraints manager: 5.45 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: 159 57.30 - 85.94: 32 85.94 - 114.59: 20 114.59 - 143.24: 16 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: 0.540 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: 2.650 Check model and map are aligned: 0.180 Process input model: 33.780 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- 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 : 16.194 143.240 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 : 1.504 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2786 time to fit residues: 143.5728 Evaluate side-chains 229 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8988 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12756 Z= 0.210 Angle : 0.633 10.639 17240 Z= 0.321 Chirality : 0.042 0.231 1952 Planarity : 0.004 0.029 2068 Dihedral : 16.884 106.388 2052 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.92 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: -2.84 (0.19), residues: 1568 helix: -1.30 (0.14), residues: 984 sheet: -2.45 (0.64), residues: 56 loop : -2.74 (0.27), residues: 528 *********************** 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 291 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 273 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 281 average time/residue: 0.2227 time to fit residues: 92.8215 Evaluate side-chains 229 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 220 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1223 time to fit residues: 3.7344 ------------------------------------------------------------------------------- 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: 9.9990 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 0.0470 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN 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: 0.7781 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 12756 Z= 0.167 Angle : 0.575 12.905 17240 Z= 0.282 Chirality : 0.040 0.161 1952 Planarity : 0.004 0.058 2068 Dihedral : 15.375 97.645 2052 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.75 % 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: -1.42 (0.21), residues: 1568 helix: 0.09 (0.16), residues: 972 sheet: -2.39 (0.60), residues: 56 loop : -2.69 (0.27), residues: 540 *********************** 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 256 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 241 average time/residue: 0.2184 time to fit residues: 79.3511 Evaluate side-chains 212 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1340 time to fit residues: 3.8926 ------------------------------------------------------------------------------- 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: 2.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12756 Z= 0.212 Angle : 0.553 8.695 17240 Z= 0.276 Chirality : 0.041 0.160 1952 Planarity : 0.003 0.035 2068 Dihedral : 14.365 93.533 2052 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.69 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: -0.58 (0.22), residues: 1568 helix: 0.82 (0.16), residues: 972 sheet: -2.31 (0.56), residues: 56 loop : -2.46 (0.28), 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 253 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 227 time to evaluate : 1.348 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 241 average time/residue: 0.2162 time to fit residues: 79.5689 Evaluate side-chains 235 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1289 time to fit residues: 6.6216 ------------------------------------------------------------------------------- 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: 2.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 691 GLN C 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 12756 Z= 0.159 Angle : 0.513 7.178 17240 Z= 0.257 Chirality : 0.040 0.144 1952 Planarity : 0.003 0.033 2068 Dihedral : 13.602 89.504 2052 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 1.84 % 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: -0.02 (0.22), residues: 1568 helix: 1.32 (0.17), residues: 956 sheet: -1.93 (0.58), 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 267 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 1.494 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 251 average time/residue: 0.2140 time to fit residues: 81.4402 Evaluate side-chains 238 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1305 time to fit residues: 5.5359 ------------------------------------------------------------------------------- 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: 0.7980 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN B 628 ASN 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: 0.7811 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12756 Z= 0.203 Angle : 0.538 5.856 17240 Z= 0.270 Chirality : 0.042 0.144 1952 Planarity : 0.003 0.028 2068 Dihedral : 13.197 92.592 2052 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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: 0.27 (0.22), residues: 1568 helix: 1.53 (0.17), residues: 960 sheet: -1.74 (0.59), residues: 56 loop : -2.15 (0.27), residues: 552 *********************** 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 256 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 1.427 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 240 average time/residue: 0.2083 time to fit residues: 75.5616 Evaluate side-chains 241 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1141 time to fit residues: 4.5018 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 E 700 GLN B 628 ASN B 700 GLN C 551 ASN C 628 ASN C 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 12756 Z= 0.154 Angle : 0.501 6.234 17240 Z= 0.255 Chirality : 0.040 0.138 1952 Planarity : 0.002 0.025 2068 Dihedral : 12.806 97.193 2052 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 1.38 % 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: 0.49 (0.22), residues: 1568 helix: 1.75 (0.17), residues: 956 sheet: -1.65 (0.59), residues: 56 loop : -2.11 (0.27), residues: 556 *********************** 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 260 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 1.331 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 251 average time/residue: 0.2155 time to fit residues: 82.1295 Evaluate side-chains 231 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1250 time to fit residues: 3.0311 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 E 691 GLN C 551 ASN C 628 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3812 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= 0.264 Angle : 0.566 6.552 17240 Z= 0.287 Chirality : 0.043 0.161 1952 Planarity : 0.003 0.025 2068 Dihedral : 12.884 108.533 2052 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % 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: 0.55 (0.22), residues: 1568 helix: 1.88 (0.17), residues: 952 sheet: -1.78 (0.59), residues: 56 loop : -2.21 (0.26), residues: 560 *********************** 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 231 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 1.595 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 222 average time/residue: 0.2231 time to fit residues: 74.6836 Evaluate side-chains 218 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1242 time to fit residues: 3.5143 ------------------------------------------------------------------------------- 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: 3.9990 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4014 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= 0.137 Angle : 0.504 8.768 17240 Z= 0.256 Chirality : 0.041 0.140 1952 Planarity : 0.002 0.019 2068 Dihedral : 12.571 112.111 2052 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.56 % 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: 0.80 (0.22), residues: 1568 helix: 2.16 (0.17), residues: 940 sheet: -1.59 (0.58), residues: 56 loop : -2.19 (0.26), residues: 572 *********************** 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 249 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.551 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 237 average time/residue: 0.2192 time to fit residues: 78.6205 Evaluate side-chains 232 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1216 time to fit residues: 3.9663 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 143 optimal weight: 0.0010 chunk 123 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- 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 B 691 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12756 Z= 0.142 Angle : 0.513 9.256 17240 Z= 0.258 Chirality : 0.041 0.146 1952 Planarity : 0.002 0.020 2068 Dihedral : 12.182 115.850 2052 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.46 % 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: 0.84 (0.22), residues: 1568 helix: 2.18 (0.17), residues: 932 sheet: -2.10 (0.57), residues: 64 loop : -2.01 (0.26), residues: 572 ********************** 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 247 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 1.326 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 246 average time/residue: 0.2137 time to fit residues: 79.6850 Evaluate side-chains 234 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1182 time to fit residues: 2.2233 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.0000 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN C 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091263 restraints weight = 22343.326| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.56 r_work: 0.2988 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12756 Z= 0.165 Angle : 0.512 9.223 17240 Z= 0.260 Chirality : 0.041 0.148 1952 Planarity : 0.002 0.021 2068 Dihedral : 12.007 116.044 2052 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 0.37 % 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: 0.92 (0.22), residues: 1568 helix: 2.24 (0.17), residues: 928 sheet: -2.05 (0.58), residues: 64 loop : -1.96 (0.26), residues: 576 =============================================================================== Job complete usr+sys time: 2498.84 seconds wall clock time: 45 minutes 54.13 seconds (2754.13 seconds total)