Starting phenix.real_space_refine on Sat Mar 16 01:05:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_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_8118/03_2024/5irz_8118_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irz_8118/03_2024/5irz_8118_trim_updated.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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-5265/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: 7.20, per 1000 atoms: 0.58 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: 5.29 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: 2.06 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: 3.06 Time building geometry restraints manager: 5.64 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 - 32.60: 7199 32.60 - 65.20: 173 65.20 - 97.80: 84 97.80 - 130.40: 60 130.40 - 163.00: 20 Dihedral angle restraints: 7536 sinusoidal: 2924 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 7533 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 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: 0.480 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: 2.270 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.710 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 23.005 163.004 4592 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 % Allowed : 1.10 % Favored : 98.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 697 HIS 0.001 0.001 HIS C 410 PHE 0.027 0.003 PHE C 448 TYR 0.017 0.002 TYR E 511 ARG 0.007 0.001 ARG D 579 *********************** 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 : 1.422 Fit side-chains REVERT: D 644 MET cc_start: 0.8298 (mmm) cc_final: 0.8086 (mmm) REVERT: D 700 GLN cc_start: 0.8087 (mt0) cc_final: 0.7846 (mt0) REVERT: E 636 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 700 GLN cc_start: 0.8094 (mt0) cc_final: 0.7877 (mt0) REVERT: B 644 MET cc_start: 0.8264 (mmm) cc_final: 0.8008 (mmm) REVERT: B 700 GLN cc_start: 0.8102 (mt0) cc_final: 0.7873 (mt0) REVERT: C 592 SER cc_start: 0.8349 (p) cc_final: 0.8024 (p) REVERT: C 700 GLN cc_start: 0.8124 (mt0) cc_final: 0.7917 (mt0) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2697 time to fit residues: 139.8727 Evaluate side-chains 229 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.2733 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= 0.213 Angle : 0.634 8.950 17240 Z= 0.321 Chirality : 0.043 0.196 1952 Planarity : 0.004 0.028 2068 Dihedral : 23.709 131.112 2292 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.65 % Allowed : 12.41 % Favored : 85.94 % 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: -2.78 (0.19), residues: 1568 helix: -1.24 (0.14), residues: 980 sheet: -2.45 (0.63), residues: 56 loop : -2.74 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 697 HIS 0.001 0.001 HIS B 410 PHE 0.020 0.001 PHE C 582 TYR 0.013 0.001 TYR D 631 ARG 0.004 0.001 ARG E 743 *********************** 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 297 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 636 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6969 (mm-30) REVERT: D 652 ASN cc_start: 0.7939 (p0) cc_final: 0.7557 (p0) REVERT: E 652 ASN cc_start: 0.8018 (p0) cc_final: 0.7665 (p0) REVERT: B 636 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7043 (mm-30) REVERT: B 652 ASN cc_start: 0.7943 (p0) cc_final: 0.7569 (p0) REVERT: C 636 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6946 (mm-30) REVERT: C 652 ASN cc_start: 0.7965 (p0) cc_final: 0.7594 (p0) outliers start: 18 outliers final: 8 residues processed: 286 average time/residue: 0.2108 time to fit residues: 89.2031 Evaluate side-chains 233 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 634 CYS 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: 10.0000 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 0.0570 chunk 153 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- 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 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** C 551 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3189 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= 0.188 Angle : 0.583 11.413 17240 Z= 0.284 Chirality : 0.041 0.158 1952 Planarity : 0.003 0.048 2068 Dihedral : 20.656 98.200 2292 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.48 % Allowed : 13.88 % Favored : 83.64 % 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: -1.44 (0.21), residues: 1568 helix: 0.06 (0.16), residues: 972 sheet: -2.37 (0.61), residues: 56 loop : -2.65 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 697 HIS 0.000 0.000 HIS E 410 PHE 0.014 0.001 PHE C 516 TYR 0.015 0.001 TYR C 511 ARG 0.005 0.000 ARG B 743 *********************** 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 262 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: D 584 TYR cc_start: 0.8281 (t80) cc_final: 0.8066 (t80) REVERT: D 636 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6904 (mm-30) REVERT: D 652 ASN cc_start: 0.7844 (p0) cc_final: 0.7619 (p0) REVERT: E 636 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6906 (mm-30) REVERT: E 652 ASN cc_start: 0.7920 (p0) cc_final: 0.7686 (p0) REVERT: B 636 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 652 ASN cc_start: 0.7822 (p0) cc_final: 0.7588 (p0) REVERT: C 652 ASN cc_start: 0.7866 (p0) cc_final: 0.7652 (p0) outliers start: 27 outliers final: 13 residues processed: 242 average time/residue: 0.2004 time to fit residues: 73.5823 Evaluate side-chains 220 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain E residue 687 ASN Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 D 691 GLN E 551 ASN E 628 ASN B 551 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN C 628 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3487 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= 0.174 Angle : 0.556 8.914 17240 Z= 0.269 Chirality : 0.040 0.144 1952 Planarity : 0.003 0.038 2068 Dihedral : 19.097 92.174 2292 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.49 % Allowed : 13.88 % Favored : 82.63 % 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: -0.50 (0.22), residues: 1568 helix: 0.89 (0.17), residues: 956 sheet: -2.28 (0.56), residues: 56 loop : -2.34 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 697 HIS 0.000 0.000 HIS D 410 PHE 0.027 0.001 PHE D 429 TYR 0.011 0.001 TYR C 511 ARG 0.003 0.000 ARG C 428 *********************** 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 282 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 1.430 Fit side-chains REVERT: D 584 TYR cc_start: 0.8410 (t80) cc_final: 0.8177 (t80) REVERT: D 636 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 652 ASN cc_start: 0.7843 (p0) cc_final: 0.7634 (p0) REVERT: E 636 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6971 (mm-30) REVERT: B 636 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7082 (mm-30) REVERT: B 652 ASN cc_start: 0.7849 (p0) cc_final: 0.7635 (p0) outliers start: 38 outliers final: 27 residues processed: 260 average time/residue: 0.1981 time to fit residues: 78.4841 Evaluate side-chains 247 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 687 ASN Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 E 551 ASN E 628 ASN ** E 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN B 628 ASN C 551 ASN C 628 ASN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3599 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= 0.228 Angle : 0.575 7.233 17240 Z= 0.278 Chirality : 0.042 0.145 1952 Planarity : 0.003 0.038 2068 Dihedral : 18.106 94.835 2292 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.58 % Allowed : 15.53 % Favored : 80.88 % 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: -0.10 (0.22), residues: 1568 helix: 1.24 (0.17), residues: 956 sheet: -2.17 (0.56), residues: 56 loop : -2.25 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 697 HIS 0.001 0.000 HIS B 410 PHE 0.030 0.001 PHE B 429 TYR 0.011 0.001 TYR B 584 ARG 0.002 0.000 ARG B 499 *********************** 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 272 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 1.431 Fit side-chains REVERT: D 636 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 636 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7049 (mm-30) REVERT: E 652 ASN cc_start: 0.7959 (p0) cc_final: 0.7648 (p0) REVERT: B 636 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7060 (mm-30) REVERT: C 652 ASN cc_start: 0.7975 (p0) cc_final: 0.7699 (p0) outliers start: 39 outliers final: 30 residues processed: 246 average time/residue: 0.2120 time to fit residues: 79.0308 Evaluate side-chains 252 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 687 ASN Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 40.0000 chunk 150 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN E 628 ASN B 551 ASN B 628 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12756 Z= 0.142 Angle : 0.516 6.700 17240 Z= 0.254 Chirality : 0.040 0.137 1952 Planarity : 0.003 0.031 2068 Dihedral : 17.334 100.609 2292 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.40 % Allowed : 17.19 % Favored : 79.41 % 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: 0.31 (0.22), residues: 1568 helix: 1.65 (0.17), residues: 952 sheet: -1.74 (0.58), residues: 56 loop : -2.25 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.000 0.000 HIS B 410 PHE 0.027 0.001 PHE C 429 TYR 0.012 0.001 TYR E 584 ARG 0.002 0.000 ARG C 428 *********************** 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 287 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 1.428 Fit side-chains REVERT: D 636 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7030 (mm-30) REVERT: E 652 ASN cc_start: 0.7839 (p0) cc_final: 0.7564 (p0) REVERT: B 636 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7024 (mm-30) REVERT: C 636 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6780 (mm-30) REVERT: C 652 ASN cc_start: 0.7850 (p0) cc_final: 0.7587 (p0) outliers start: 37 outliers final: 25 residues processed: 257 average time/residue: 0.2089 time to fit residues: 81.1734 Evaluate side-chains 252 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 553 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 0.0970 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN B 551 ASN B 652 ASN C 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12756 Z= 0.149 Angle : 0.510 5.790 17240 Z= 0.253 Chirality : 0.040 0.146 1952 Planarity : 0.002 0.025 2068 Dihedral : 16.559 108.062 2292 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.31 % Allowed : 18.57 % Favored : 78.12 % 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: 0.44 (0.22), residues: 1568 helix: 1.75 (0.17), residues: 972 sheet: -1.57 (0.59), residues: 56 loop : -2.37 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.000 0.000 HIS B 410 PHE 0.028 0.001 PHE C 429 TYR 0.011 0.001 TYR D 584 ARG 0.002 0.000 ARG B 499 *********************** 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 280 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 1.327 Fit side-chains REVERT: D 636 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7109 (mm-30) REVERT: E 652 ASN cc_start: 0.7841 (p0) cc_final: 0.7566 (p0) REVERT: B 636 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 652 ASN cc_start: 0.7863 (p0) cc_final: 0.7601 (p0) outliers start: 36 outliers final: 21 residues processed: 251 average time/residue: 0.1990 time to fit residues: 75.5906 Evaluate side-chains 256 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 687 ASN Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN E 551 ASN B 551 ASN C 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12756 Z= 0.233 Angle : 0.548 7.020 17240 Z= 0.272 Chirality : 0.043 0.197 1952 Planarity : 0.003 0.028 2068 Dihedral : 16.256 117.679 2292 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.67 % Allowed : 19.49 % Favored : 77.85 % 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: 0.44 (0.22), residues: 1568 helix: 1.74 (0.17), residues: 980 sheet: -1.63 (0.59), residues: 56 loop : -2.38 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 697 HIS 0.001 0.000 HIS C 410 PHE 0.029 0.001 PHE C 429 TYR 0.012 0.001 TYR D 671 ARG 0.003 0.000 ARG E 499 *********************** 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 258 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.518 Fit side-chains REVERT: D 636 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7047 (mm-30) REVERT: E 652 ASN cc_start: 0.8030 (p0) cc_final: 0.7759 (p0) REVERT: B 636 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7028 (mm-30) REVERT: B 644 MET cc_start: 0.8164 (mmm) cc_final: 0.7597 (mmm) REVERT: C 652 ASN cc_start: 0.7995 (p0) cc_final: 0.7726 (p0) outliers start: 29 outliers final: 25 residues processed: 234 average time/residue: 0.2150 time to fit residues: 75.3737 Evaluate side-chains 245 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 0.0040 chunk 84 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN E 551 ASN B 551 ASN C 551 ASN C 691 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4226 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= 0.128 Angle : 0.487 7.165 17240 Z= 0.246 Chirality : 0.040 0.154 1952 Planarity : 0.002 0.019 2068 Dihedral : 15.557 120.811 2292 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.76 % Allowed : 19.49 % Favored : 77.76 % 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: 0.79 (0.22), residues: 1568 helix: 2.09 (0.17), residues: 944 sheet: -1.37 (0.58), residues: 56 loop : -2.12 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 697 HIS 0.000 0.000 HIS D 410 PHE 0.034 0.001 PHE C 429 TYR 0.014 0.001 TYR D 472 ARG 0.002 0.000 ARG B 499 *********************** 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 269 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.444 Fit side-chains REVERT: D 636 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 636 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 644 MET cc_start: 0.8083 (mmm) cc_final: 0.7583 (mmm) outliers start: 30 outliers final: 17 residues processed: 245 average time/residue: 0.2086 time to fit residues: 76.8802 Evaluate side-chains 249 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.4980 chunk 90 optimal weight: 0.0170 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 12 optimal weight: 0.0040 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 98 optimal weight: 0.0060 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN B 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12756 Z= 0.131 Angle : 0.496 6.425 17240 Z= 0.254 Chirality : 0.040 0.170 1952 Planarity : 0.002 0.024 2068 Dihedral : 14.849 122.114 2292 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.02 % Allowed : 20.96 % Favored : 77.02 % 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: 0.86 (0.22), residues: 1568 helix: 2.27 (0.17), residues: 936 sheet: -1.81 (0.60), residues: 64 loop : -2.23 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 549 HIS 0.000 0.000 HIS D 410 PHE 0.033 0.001 PHE C 429 TYR 0.017 0.001 TYR E 351 ARG 0.002 0.000 ARG D 499 ********************** 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 279 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 1.398 Fit side-chains REVERT: D 636 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7028 (mm-30) REVERT: B 574 LEU cc_start: 0.8522 (mt) cc_final: 0.8306 (mt) REVERT: B 636 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 644 MET cc_start: 0.8064 (mmm) cc_final: 0.7607 (mmm) outliers start: 22 outliers final: 19 residues processed: 260 average time/residue: 0.2018 time to fit residues: 79.4121 Evaluate side-chains 249 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN C 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092115 restraints weight = 22425.424| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.60 r_work: 0.2992 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12756 Z= 0.162 Angle : 0.531 10.805 17240 Z= 0.263 Chirality : 0.041 0.149 1952 Planarity : 0.002 0.022 2068 Dihedral : 14.678 124.501 2292 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.30 % Allowed : 21.60 % Favored : 76.10 % 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: 0.91 (0.22), residues: 1568 helix: 2.30 (0.17), residues: 936 sheet: -1.68 (0.61), residues: 64 loop : -2.19 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 697 HIS 0.001 0.000 HIS C 410 PHE 0.033 0.001 PHE C 429 TYR 0.013 0.001 TYR C 472 ARG 0.002 0.000 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.41 seconds wall clock time: 46 minutes 39.60 seconds (2799.60 seconds total)