Starting phenix.real_space_refine on Thu Feb 5 15:22:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rms_54065/02_2026/9rms_54065.map" } resolution = 3.8 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 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= 0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11786 2.51 5 N 2920 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18061 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3127 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 383} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3132 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3163 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1379 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1332 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1370 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1371 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 176} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.00, per 1000 atoms: 0.22 Number of scatterers: 18061 At special positions: 0 Unit cell: (119.547, 116.962, 139.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3227 8.00 N 2920 7.00 C 11786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS D 611 " distance=2.21 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.06 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 669.0 milliseconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 24 sheets defined 58.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 438 through 441 removed outlier: 4.086A pdb=" N ASP A 441 " --> pdb=" O GLU A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 445 through 458 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 544 through 568 Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.030A pdb=" N TRP A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.649A pdb=" N TRP A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 652 removed outlier: 3.760A pdb=" N THR A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.806A pdb=" N GLU A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 4.417A pdb=" N MET A 692 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 717 Processing helix chain 'A' and resid 727 through 736 Processing helix chain 'A' and resid 764 through 778 removed outlier: 3.658A pdb=" N ALA A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 790 removed outlier: 3.516A pdb=" N LEU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 842 removed outlier: 3.806A pdb=" N TYR A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 842 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 544 through 569 removed outlier: 4.415A pdb=" N SER B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 617 through 652 Processing helix chain 'B' and resid 658 through 663 Processing helix chain 'B' and resid 675 through 684 removed outlier: 3.642A pdb=" N PHE B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 699 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.704A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 790 Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.712A pdb=" N TYR B 819 " --> pdb=" O ALA B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 544 through 568 removed outlier: 3.545A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.737A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 648 removed outlier: 3.896A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 764 through 778 removed outlier: 3.585A pdb=" N LEU C 770 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 815 through 842 removed outlier: 3.586A pdb=" N TYR C 819 " --> pdb=" O ALA C 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 441 removed outlier: 3.800A pdb=" N ASP D 441 " --> pdb=" O GLU D 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 441' Processing helix chain 'D' and resid 445 through 459 removed outlier: 3.577A pdb=" N SER D 452 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 491 removed outlier: 3.532A pdb=" N LEU D 489 " --> pdb=" O MET D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 544 through 569 removed outlier: 3.535A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER D 569 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.887A pdb=" N LEU D 599 " --> pdb=" O ILE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 646 removed outlier: 3.518A pdb=" N ALA D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 664 removed outlier: 3.939A pdb=" N GLN D 664 " --> pdb=" O ASP D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 removed outlier: 3.588A pdb=" N GLU D 679 " --> pdb=" O GLY D 675 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 681 " --> pdb=" O THR D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 698 removed outlier: 3.533A pdb=" N SER D 698 " --> pdb=" O THR D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 764 through 779 Processing helix chain 'D' and resid 779 through 790 removed outlier: 3.597A pdb=" N LYS D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 843 removed outlier: 4.149A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.955A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 125 removed outlier: 3.954A pdb=" N VAL E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 4.013A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 211 Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.829A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 4.054A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 Processing helix chain 'G' and resid 8 through 30 Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.501A pdb=" N SER G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.555A pdb=" N ILE G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.634A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 Processing helix chain 'H' and resid 8 through 30 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.841A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 removed outlier: 3.508A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.953A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 527 removed outlier: 4.076A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 670 removed outlier: 6.597A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 463 through 466 removed outlier: 6.224A pdb=" N VAL B 419 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 520 removed outlier: 3.955A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 668 through 670 removed outlier: 6.683A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 462 through 466 removed outlier: 6.547A pdb=" N VAL C 417 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA C 465 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB4, first strand: chain 'C' and resid 512 through 513 removed outlier: 3.538A pdb=" N ASP C 512 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 518 through 520 removed outlier: 3.851A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.580A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 417 through 419 removed outlier: 6.299A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB9, first strand: chain 'D' and resid 501 through 502 removed outlier: 4.277A pdb=" N LEU D 501 " --> pdb=" O GLY D 755 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AC2, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.569A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.575A pdb=" N GLY E 38 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.921A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS F 60 " --> pdb=" O CYS F 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 77 through 79 removed outlier: 3.610A pdb=" N CYS G 67 " --> pdb=" O HIS G 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 57 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.939A pdb=" N CYS H 67 " --> pdb=" O HIS H 60 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3120 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: 3.69 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4820 1.33 - 1.46: 5147 1.46 - 1.59: 8298 1.59 - 1.72: 5 1.72 - 1.85: 208 Bond restraints: 18478 Sorted by residual: bond pdb=" CA PRO C 759 " pdb=" C PRO C 759 " ideal model delta sigma weight residual 1.521 1.599 -0.079 9.30e-03 1.16e+04 7.14e+01 bond pdb=" N PRO C 759 " pdb=" CA PRO C 759 " ideal model delta sigma weight residual 1.470 1.526 -0.057 1.01e-02 9.80e+03 3.14e+01 bond pdb=" CA LYS C 760 " pdb=" C LYS C 760 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.33e+01 bond pdb=" CA VAL C 448 " pdb=" CB VAL C 448 " ideal model delta sigma weight residual 1.540 1.580 -0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" N VAL D 652 " pdb=" CA VAL D 652 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 ... (remaining 18473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 24867 3.74 - 7.48: 126 7.48 - 11.22: 6 11.22 - 14.96: 2 14.96 - 18.70: 1 Bond angle restraints: 25002 Sorted by residual: angle pdb=" C LYS C 760 " pdb=" N GLY C 761 " pdb=" CA GLY C 761 " ideal model delta sigma weight residual 121.93 103.23 18.70 1.94e+00 2.66e-01 9.29e+01 angle pdb=" C THR C 758 " pdb=" N PRO C 759 " pdb=" CA PRO C 759 " ideal model delta sigma weight residual 120.79 132.45 -11.66 1.30e+00 5.92e-01 8.04e+01 angle pdb=" N PRO C 759 " pdb=" CA PRO C 759 " pdb=" C PRO C 759 " ideal model delta sigma weight residual 110.74 121.90 -11.16 1.66e+00 3.63e-01 4.52e+01 angle pdb=" C THR B 707 " pdb=" N THR B 708 " pdb=" CA THR B 708 " ideal model delta sigma weight residual 120.29 111.08 9.21 1.42e+00 4.96e-01 4.21e+01 angle pdb=" C PRO C 759 " pdb=" N LYS C 760 " pdb=" CA LYS C 760 " ideal model delta sigma weight residual 121.54 133.72 -12.18 1.91e+00 2.74e-01 4.07e+01 ... (remaining 24997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 10073 17.56 - 35.11: 573 35.11 - 52.67: 109 52.67 - 70.23: 48 70.23 - 87.79: 7 Dihedral angle restraints: 10810 sinusoidal: 4154 harmonic: 6656 Sorted by residual: dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS C 611 " pdb=" CB CYS C 611 " ideal model delta sinusoidal sigma weight residual 93.00 5.21 87.79 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -37.49 -48.51 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CA PRO C 759 " pdb=" C PRO C 759 " pdb=" N LYS C 760 " pdb=" CA LYS C 760 " ideal model delta harmonic sigma weight residual 180.00 -153.14 -26.86 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 10807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2259 0.061 - 0.122: 428 0.122 - 0.183: 84 0.183 - 0.244: 34 0.244 - 0.304: 2 Chirality restraints: 2807 Sorted by residual: chirality pdb=" CA THR B 766 " pdb=" N THR B 766 " pdb=" C THR B 766 " pdb=" CB THR B 766 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA SER B 718 " pdb=" N SER B 718 " pdb=" C SER B 718 " pdb=" CB SER B 718 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLU B 435 " pdb=" N GLU B 435 " pdb=" C GLU B 435 " pdb=" CB GLU B 435 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2804 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 757 " -0.027 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C ALA C 757 " 0.099 2.00e-02 2.50e+03 pdb=" O ALA C 757 " -0.038 2.00e-02 2.50e+03 pdb=" N THR C 758 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 102 " -0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG H 102 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG H 102 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG H 102 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 102 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 758 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C THR C 758 " 0.064 2.00e-02 2.50e+03 pdb=" O THR C 758 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO C 759 " -0.022 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 5 2.14 - 2.83: 5765 2.83 - 3.52: 25318 3.52 - 4.21: 41357 4.21 - 4.90: 73996 Nonbonded interactions: 146441 Sorted by model distance: nonbonded pdb=" CG2 VAL C 715 " pdb=" CD2 PHE C 724 " model vdw 1.454 3.760 nonbonded pdb=" CG LYS C 515 " pdb=" CE MET D 436 " model vdw 1.688 3.860 nonbonded pdb=" CG2 VAL C 715 " pdb=" CE2 PHE C 724 " model vdw 1.889 3.760 nonbonded pdb=" OE2 GLU C 424 " pdb=" O16 E2Q C1001 " model vdw 2.090 3.040 nonbonded pdb=" OE2 GLU A 546 " pdb=" OH TYR H 174 " model vdw 2.093 3.040 ... (remaining 146436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 419 through 429 or (resid 430 and (name N or name CA or na \ me C or name O or name CB )) or resid 431 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 through 487 or (resid \ 488 and (name N or name CA or name C or name O or name CB )) or resid 489 throug \ h 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) or \ resid 513 through 528 or resid 533 through 648 or (resid 649 through 650 and (na \ me N or name CA or name C or name O or name CB )) or resid 651 or (resid 652 thr \ ough 653 and (name N or name CA or name C or name O or name CB )) or resid 654 o \ r resid 657 through 723 or (resid 724 and (name N or name CA or name C or name O \ or name CB )) or resid 725 through 726 or (resid 727 and (name N or name CA or \ name C or name O or name CB )) or resid 728 through 764 or (resid 765 and (name \ N or name CA or name C or name O or name CB )) or resid 766 through 1001)) selection = (chain 'B' and (resid 419 through 511 or (resid 512 and (name N or name CA or na \ me C or name O or name CB )) or resid 513 through 648 or (resid 649 through 650 \ and (name N or name CA or name C or name O or name CB )) or resid 651 through 76 \ 4 or (resid 765 and (name N or name CA or name C or name O or name CB )) or resi \ d 766 through 796 or resid 808 through 1001)) selection = (chain 'C' and (resid 419 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 487 or (resid 488 and (name N \ or name CA or name C or name O or name CB )) or resid 489 through 651 or (resid \ 652 through 653 and (name N or name CA or name C or name O or name CB )) or resi \ d 654 or resid 657 through 723 or (resid 724 and (name N or name CA or name C or \ name O or name CB )) or resid 725 through 726 or (resid 727 and (name N or name \ CA or name C or name O or name CB )) or resid 728 through 796 or resid 808 thro \ ugh 1001)) selection = (chain 'D' and (resid 419 through 429 or (resid 430 and (name N or name CA or na \ me C or name O or name CB )) or resid 431 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 through 487 or (resid \ 488 and (name N or name CA or name C or name O or name CB )) or resid 489 throug \ h 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) or \ resid 513 through 528 or resid 533 through 648 or (resid 649 through 650 and (na \ me N or name CA or name C or name O or name CB )) or resid 651 or (resid 652 thr \ ough 653 and (name N or name CA or name C or name O or name CB )) or resid 654 o \ r resid 657 through 723 or (resid 724 and (name N or name CA or name C or name O \ or name CB )) or resid 725 through 726 or (resid 727 and (name N or name CA or \ name C or name O or name CB )) or resid 728 through 764 or (resid 765 and (name \ N or name CA or name C or name O or name CB )) or resid 766 through 796 or resid \ 808 through 1001)) } ncs_group { reference = (chain 'E' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 41 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 71 or (resid 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and \ (name N or name CA or name C or name O or name CB )) or resid 75 through 81 or ( \ resid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 161 or resid 173 through 212)) selection = (chain 'F' and (resid 7 through 40 or (resid 41 through 56 and (name N or name C \ A or name C or name O or name CB )) or resid 57 through 71 or (resid 72 and (nam \ e N or name CA or name C or name O or name CB )) or resid 73 through 161 or resi \ d 173 through 212)) selection = (chain 'G' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 41 or resid 56 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 through \ 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or res \ id 83 through 96 or (resid 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 161 or resid 173 through 212)) selection = (chain 'H' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 81 or (resid 82 and (name N or n \ ame CA or name C or name O or name CB )) or resid 83 through 96 or (resid 97 and \ (name N or name CA or name C or name O or name CB )) or resid 98 through 161 or \ resid 173 through 212)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 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 : 0.009 0.778 18493 Z= 0.694 Angle : 0.762 18.696 25030 Z= 0.484 Chirality : 0.053 0.304 2807 Planarity : 0.009 0.185 3066 Dihedral : 12.156 84.698 6510 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 0.27 % Allowed : 0.74 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.17), residues: 2260 helix: -0.19 (0.14), residues: 1301 sheet: -1.90 (0.41), residues: 139 loop : -2.63 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG G 209 TYR 0.041 0.002 TYR C 491 PHE 0.037 0.001 PHE B 513 TRP 0.032 0.002 TRP C 788 HIS 0.004 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00616 (18478) covalent geometry : angle 0.76118 (25002) SS BOND : bond 0.04969 ( 14) SS BOND : angle 1.46667 ( 28) hydrogen bonds : bond 0.22692 ( 1066) hydrogen bonds : angle 7.21035 ( 3120) Misc. bond : bond 0.77825 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 495 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 185 LEU cc_start: 0.8866 (tp) cc_final: 0.8662 (tt) REVERT: H 156 TYR cc_start: 0.7764 (t80) cc_final: 0.7518 (t80) outliers start: 5 outliers final: 0 residues processed: 499 average time/residue: 0.1452 time to fit residues: 105.1916 Evaluate side-chains 248 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS A 608 GLN A 641 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.062877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044934 restraints weight = 99695.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046311 restraints weight = 54107.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047210 restraints weight = 35609.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047781 restraints weight = 26581.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048206 restraints weight = 21664.831| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18493 Z= 0.256 Angle : 0.710 9.915 25030 Z= 0.374 Chirality : 0.043 0.193 2807 Planarity : 0.005 0.048 3066 Dihedral : 5.432 58.075 2539 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 12.12 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2260 helix: 1.33 (0.14), residues: 1320 sheet: -1.37 (0.39), residues: 171 loop : -2.00 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 507 TYR 0.024 0.002 TYR G 176 PHE 0.032 0.002 PHE C 724 TRP 0.022 0.002 TRP C 573 HIS 0.008 0.002 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00535 (18478) covalent geometry : angle 0.70584 (25002) SS BOND : bond 0.00533 ( 14) SS BOND : angle 2.32211 ( 28) hydrogen bonds : bond 0.04982 ( 1066) hydrogen bonds : angle 4.60420 ( 3120) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.9530 (tpp) cc_final: 0.8999 (mmt) REVERT: A 727 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8773 (mp0) REVERT: A 730 MET cc_start: 0.7857 (mmm) cc_final: 0.7599 (mmm) REVERT: B 423 MET cc_start: 0.8616 (mmt) cc_final: 0.8342 (mmm) REVERT: B 631 THR cc_start: 0.9585 (m) cc_final: 0.9320 (p) REVERT: C 423 MET cc_start: 0.8469 (mmm) cc_final: 0.8260 (tpp) REVERT: C 436 MET cc_start: 0.8737 (ptp) cc_final: 0.8433 (ppp) REVERT: C 515 LYS cc_start: 0.9034 (mptt) cc_final: 0.8460 (tttm) REVERT: C 729 THR cc_start: 0.9683 (p) cc_final: 0.9438 (t) REVERT: C 835 GLU cc_start: 0.8837 (tp30) cc_final: 0.8620 (tm-30) REVERT: D 607 MET cc_start: 0.9209 (mmt) cc_final: 0.8732 (mmm) REVERT: D 608 GLN cc_start: 0.9109 (mp10) cc_final: 0.8703 (mp10) REVERT: D 730 MET cc_start: 0.8954 (mmm) cc_final: 0.8730 (mmm) REVERT: D 743 MET cc_start: 0.9400 (ptt) cc_final: 0.9200 (ppp) REVERT: F 33 TRP cc_start: 0.8993 (m100) cc_final: 0.8501 (m100) REVERT: G 117 MET cc_start: 0.8266 (tpp) cc_final: 0.8062 (tpp) REVERT: G 149 ASN cc_start: 0.9550 (t0) cc_final: 0.9299 (t0) REVERT: G 203 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9164 (m-30) REVERT: G 206 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8848 (mtmm) REVERT: H 24 MET cc_start: 0.9610 (tpp) cc_final: 0.9065 (tpp) REVERT: H 120 LEU cc_start: 0.9630 (mt) cc_final: 0.9409 (mt) outliers start: 43 outliers final: 29 residues processed: 275 average time/residue: 0.1381 time to fit residues: 55.6560 Evaluate side-chains 229 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 751 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 203 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044759 restraints weight = 99206.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046087 restraints weight = 53644.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047004 restraints weight = 35577.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047586 restraints weight = 26288.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047958 restraints weight = 21274.811| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18493 Z= 0.170 Angle : 0.608 8.487 25030 Z= 0.315 Chirality : 0.041 0.231 2807 Planarity : 0.004 0.047 3066 Dihedral : 5.195 57.805 2539 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.29 % Allowed : 13.40 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2260 helix: 1.92 (0.14), residues: 1332 sheet: -1.18 (0.40), residues: 171 loop : -1.65 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 706 TYR 0.016 0.001 TYR G 176 PHE 0.020 0.001 PHE C 724 TRP 0.016 0.001 TRP D 573 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00365 (18478) covalent geometry : angle 0.60565 (25002) SS BOND : bond 0.00616 ( 14) SS BOND : angle 1.56215 ( 28) hydrogen bonds : bond 0.04349 ( 1066) hydrogen bonds : angle 4.20728 ( 3120) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8708 (mpp) REVERT: A 607 MET cc_start: 0.9467 (tpp) cc_final: 0.8845 (mmt) REVERT: A 637 SER cc_start: 0.9842 (m) cc_final: 0.9537 (p) REVERT: A 727 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8698 (mp0) REVERT: A 743 MET cc_start: 0.9266 (ppp) cc_final: 0.8872 (ppp) REVERT: B 423 MET cc_start: 0.8659 (mmt) cc_final: 0.8268 (mmm) REVERT: B 631 THR cc_start: 0.9523 (m) cc_final: 0.9230 (p) REVERT: B 730 MET cc_start: 0.9120 (tpt) cc_final: 0.8859 (ptm) REVERT: C 436 MET cc_start: 0.8746 (ptp) cc_final: 0.8369 (ppp) REVERT: C 515 LYS cc_start: 0.8983 (mptt) cc_final: 0.8470 (tttt) REVERT: C 696 MET cc_start: 0.8085 (ptp) cc_final: 0.7866 (ptm) REVERT: C 835 GLU cc_start: 0.8800 (tp30) cc_final: 0.8551 (tm-30) REVERT: D 607 MET cc_start: 0.9274 (mmt) cc_final: 0.8899 (mmt) REVERT: D 608 GLN cc_start: 0.9072 (mp10) cc_final: 0.8770 (mp10) REVERT: D 730 MET cc_start: 0.8979 (mmm) cc_final: 0.8719 (mmm) REVERT: E 24 MET cc_start: 0.9164 (tpt) cc_final: 0.8948 (tpt) REVERT: E 70 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8677 (mp0) REVERT: F 23 LEU cc_start: 0.9723 (tp) cc_final: 0.9440 (tp) REVERT: F 24 MET cc_start: 0.9599 (mmm) cc_final: 0.9186 (tpp) REVERT: F 33 TRP cc_start: 0.8973 (m100) cc_final: 0.8622 (m100) REVERT: F 149 ASN cc_start: 0.9596 (t0) cc_final: 0.9392 (t0) REVERT: F 206 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8975 (ptpt) REVERT: G 33 TRP cc_start: 0.9181 (m100) cc_final: 0.8845 (m100) REVERT: G 117 MET cc_start: 0.8377 (tpp) cc_final: 0.8069 (tpp) REVERT: G 206 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8958 (mtmt) REVERT: G 207 GLN cc_start: 0.9041 (mt0) cc_final: 0.8763 (pt0) REVERT: H 120 LEU cc_start: 0.9623 (mt) cc_final: 0.9398 (mt) outliers start: 43 outliers final: 22 residues processed: 249 average time/residue: 0.1247 time to fit residues: 47.3942 Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 751 SER Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 82 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 225 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043895 restraints weight = 100618.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045168 restraints weight = 55703.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046017 restraints weight = 37533.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046538 restraints weight = 28185.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046962 restraints weight = 23162.723| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18493 Z= 0.188 Angle : 0.610 7.886 25030 Z= 0.315 Chirality : 0.040 0.160 2807 Planarity : 0.004 0.061 3066 Dihedral : 5.037 47.655 2539 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.34 % Allowed : 14.25 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2260 helix: 2.22 (0.14), residues: 1335 sheet: -0.98 (0.39), residues: 164 loop : -1.48 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 37 TYR 0.017 0.001 TYR C 754 PHE 0.019 0.001 PHE C 681 TRP 0.013 0.001 TRP A 788 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00403 (18478) covalent geometry : angle 0.60494 (25002) SS BOND : bond 0.00467 ( 14) SS BOND : angle 2.36775 ( 28) hydrogen bonds : bond 0.04057 ( 1066) hydrogen bonds : angle 4.12955 ( 3120) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8732 (mpp) REVERT: A 607 MET cc_start: 0.9452 (tpp) cc_final: 0.8839 (mmt) REVERT: A 637 SER cc_start: 0.9832 (m) cc_final: 0.9572 (p) REVERT: A 743 MET cc_start: 0.9309 (ppp) cc_final: 0.8956 (ppp) REVERT: B 423 MET cc_start: 0.8689 (mmt) cc_final: 0.8301 (mmm) REVERT: B 631 THR cc_start: 0.9480 (m) cc_final: 0.9265 (p) REVERT: B 651 MET cc_start: 0.8995 (tpp) cc_final: 0.8693 (mmt) REVERT: C 423 MET cc_start: 0.8069 (tpp) cc_final: 0.7805 (tpp) REVERT: C 436 MET cc_start: 0.8779 (ptp) cc_final: 0.8407 (ppp) REVERT: C 515 LYS cc_start: 0.8977 (mptt) cc_final: 0.8377 (tttp) REVERT: C 692 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.9012 (mpp) REVERT: C 835 GLU cc_start: 0.8738 (tp30) cc_final: 0.8514 (tm-30) REVERT: D 518 MET cc_start: 0.8507 (ptm) cc_final: 0.8244 (ppp) REVERT: D 607 MET cc_start: 0.9316 (mmt) cc_final: 0.8666 (mmm) REVERT: D 608 GLN cc_start: 0.9041 (mp10) cc_final: 0.8749 (mp10) REVERT: D 730 MET cc_start: 0.8984 (mmm) cc_final: 0.8721 (mmm) REVERT: E 10 MET cc_start: 0.9240 (tpp) cc_final: 0.8897 (tpp) REVERT: E 24 MET cc_start: 0.9173 (tpt) cc_final: 0.8972 (tpt) REVERT: F 24 MET cc_start: 0.9578 (mmm) cc_final: 0.9237 (tpp) REVERT: F 33 TRP cc_start: 0.8986 (m100) cc_final: 0.8523 (m100) REVERT: F 206 LYS cc_start: 0.9281 (mtmm) cc_final: 0.8921 (ptpp) REVERT: G 24 MET cc_start: 0.9429 (tpp) cc_final: 0.9163 (mmm) REVERT: G 33 TRP cc_start: 0.9155 (m100) cc_final: 0.8767 (m100) REVERT: G 117 MET cc_start: 0.8378 (tpp) cc_final: 0.8018 (tpp) REVERT: G 206 LYS cc_start: 0.9300 (mtmt) cc_final: 0.8961 (mtmt) REVERT: H 24 MET cc_start: 0.9575 (tpp) cc_final: 0.9047 (tpp) REVERT: H 120 LEU cc_start: 0.9617 (mt) cc_final: 0.9385 (mt) outliers start: 44 outliers final: 29 residues processed: 241 average time/residue: 0.1288 time to fit residues: 47.7482 Evaluate side-chains 221 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 217 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 ASN E 132 HIS ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.060542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043069 restraints weight = 102142.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044379 restraints weight = 55103.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.045229 restraints weight = 36197.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045737 restraints weight = 26902.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046173 restraints weight = 22070.698| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18493 Z= 0.199 Angle : 0.599 8.354 25030 Z= 0.311 Chirality : 0.040 0.207 2807 Planarity : 0.004 0.043 3066 Dihedral : 4.782 38.137 2539 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.45 % Allowed : 15.84 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2260 helix: 2.28 (0.14), residues: 1338 sheet: -1.06 (0.39), residues: 171 loop : -1.35 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 507 TYR 0.016 0.001 TYR G 156 PHE 0.014 0.001 PHE D 563 TRP 0.012 0.001 TRP A 788 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00427 (18478) covalent geometry : angle 0.59733 (25002) SS BOND : bond 0.00472 ( 14) SS BOND : angle 1.43616 ( 28) hydrogen bonds : bond 0.03972 ( 1066) hydrogen bonds : angle 4.14726 ( 3120) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.9432 (tpp) cc_final: 0.8738 (mmt) REVERT: A 637 SER cc_start: 0.9830 (m) cc_final: 0.9579 (p) REVERT: A 743 MET cc_start: 0.9352 (ppp) cc_final: 0.8982 (ppp) REVERT: B 423 MET cc_start: 0.8733 (mmt) cc_final: 0.8342 (mmm) REVERT: B 485 MET cc_start: 0.8300 (mmm) cc_final: 0.8052 (mmm) REVERT: B 541 ASP cc_start: 0.8927 (m-30) cc_final: 0.8678 (m-30) REVERT: B 607 MET cc_start: 0.9322 (ttm) cc_final: 0.9100 (mtt) REVERT: B 631 THR cc_start: 0.9501 (m) cc_final: 0.9158 (p) REVERT: B 730 MET cc_start: 0.9146 (tpt) cc_final: 0.8476 (mmm) REVERT: C 423 MET cc_start: 0.7995 (tpp) cc_final: 0.7731 (tpp) REVERT: C 429 MET cc_start: 0.8281 (mpp) cc_final: 0.7930 (mpp) REVERT: C 436 MET cc_start: 0.8831 (ptp) cc_final: 0.8554 (ppp) REVERT: C 515 LYS cc_start: 0.8987 (mptt) cc_final: 0.8416 (tttt) REVERT: D 518 MET cc_start: 0.8587 (ptm) cc_final: 0.8255 (ppp) REVERT: D 607 MET cc_start: 0.9288 (mmt) cc_final: 0.8779 (mmm) REVERT: D 608 GLN cc_start: 0.9118 (mp10) cc_final: 0.8825 (mp10) REVERT: D 651 MET cc_start: 0.8895 (ttm) cc_final: 0.8660 (ttm) REVERT: E 10 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8932 (tpp) REVERT: F 23 LEU cc_start: 0.9731 (tp) cc_final: 0.9455 (tp) REVERT: F 24 MET cc_start: 0.9612 (mmm) cc_final: 0.9054 (tpp) REVERT: F 33 TRP cc_start: 0.9007 (m100) cc_final: 0.8584 (m100) REVERT: F 117 MET cc_start: 0.8303 (tpt) cc_final: 0.7994 (tpt) REVERT: F 203 ASP cc_start: 0.9239 (m-30) cc_final: 0.8772 (m-30) REVERT: G 33 TRP cc_start: 0.9194 (m100) cc_final: 0.8767 (m100) REVERT: G 117 MET cc_start: 0.8428 (tpp) cc_final: 0.8043 (tpp) REVERT: G 206 LYS cc_start: 0.9327 (mtmt) cc_final: 0.8978 (mtmt) REVERT: H 10 MET cc_start: 0.9134 (mmm) cc_final: 0.8645 (tpp) REVERT: H 120 LEU cc_start: 0.9617 (mt) cc_final: 0.9384 (mt) outliers start: 46 outliers final: 29 residues processed: 234 average time/residue: 0.1227 time to fit residues: 45.3392 Evaluate side-chains 219 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.061259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043854 restraints weight = 99976.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045208 restraints weight = 53547.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046044 restraints weight = 35041.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046574 restraints weight = 26007.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047000 restraints weight = 21301.872| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18493 Z= 0.137 Angle : 0.589 9.654 25030 Z= 0.297 Chirality : 0.040 0.213 2807 Planarity : 0.004 0.043 3066 Dihedral : 5.022 52.598 2539 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 16.59 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2260 helix: 2.45 (0.14), residues: 1338 sheet: -0.98 (0.40), residues: 160 loop : -1.28 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 507 TYR 0.017 0.001 TYR G 156 PHE 0.015 0.001 PHE C 681 TRP 0.011 0.001 TRP A 788 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00299 (18478) covalent geometry : angle 0.58708 (25002) SS BOND : bond 0.00391 ( 14) SS BOND : angle 1.56779 ( 28) hydrogen bonds : bond 0.03764 ( 1066) hydrogen bonds : angle 3.95562 ( 3120) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8991 (mpp) cc_final: 0.8436 (mpp) REVERT: A 518 MET cc_start: 0.8759 (ttm) cc_final: 0.8504 (mtt) REVERT: A 525 MET cc_start: 0.8647 (ppp) cc_final: 0.8332 (ppp) REVERT: A 607 MET cc_start: 0.9414 (tpp) cc_final: 0.8658 (mmt) REVERT: A 637 SER cc_start: 0.9823 (m) cc_final: 0.9566 (p) REVERT: A 743 MET cc_start: 0.9363 (ppp) cc_final: 0.8977 (ppp) REVERT: B 423 MET cc_start: 0.8725 (mmt) cc_final: 0.8329 (mmm) REVERT: B 436 MET cc_start: 0.9230 (ptp) cc_final: 0.8497 (ppp) REVERT: B 485 MET cc_start: 0.8369 (mmm) cc_final: 0.8138 (mmm) REVERT: B 518 MET cc_start: 0.7847 (mmm) cc_final: 0.7568 (mmm) REVERT: B 607 MET cc_start: 0.9297 (ttm) cc_final: 0.9031 (mtt) REVERT: B 631 THR cc_start: 0.9473 (m) cc_final: 0.9201 (p) REVERT: B 730 MET cc_start: 0.9096 (tpt) cc_final: 0.8404 (mmm) REVERT: C 423 MET cc_start: 0.7961 (tpp) cc_final: 0.7664 (tpp) REVERT: C 429 MET cc_start: 0.8263 (mpp) cc_final: 0.7894 (mpp) REVERT: C 436 MET cc_start: 0.8823 (ptp) cc_final: 0.8612 (ppp) REVERT: D 518 MET cc_start: 0.8635 (ptm) cc_final: 0.8287 (ppp) REVERT: D 607 MET cc_start: 0.9272 (mmt) cc_final: 0.8789 (mmm) REVERT: D 608 GLN cc_start: 0.9159 (mp10) cc_final: 0.8876 (mp10) REVERT: D 651 MET cc_start: 0.8822 (ttm) cc_final: 0.8608 (ttm) REVERT: D 730 MET cc_start: 0.8873 (mmm) cc_final: 0.8599 (mmm) REVERT: E 10 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8851 (tpp) REVERT: F 24 MET cc_start: 0.9593 (mmm) cc_final: 0.9292 (tpp) REVERT: F 33 TRP cc_start: 0.8949 (m100) cc_final: 0.8540 (m100) REVERT: F 117 MET cc_start: 0.8274 (tpt) cc_final: 0.7969 (tpt) REVERT: F 203 ASP cc_start: 0.9206 (m-30) cc_final: 0.8697 (m-30) REVERT: G 33 TRP cc_start: 0.9096 (m100) cc_final: 0.8636 (m100) REVERT: G 117 MET cc_start: 0.8391 (tpp) cc_final: 0.7983 (tpp) REVERT: H 10 MET cc_start: 0.9075 (mmm) cc_final: 0.8555 (tpp) REVERT: H 120 LEU cc_start: 0.9600 (mt) cc_final: 0.9393 (mt) outliers start: 40 outliers final: 28 residues processed: 232 average time/residue: 0.1181 time to fit residues: 42.9887 Evaluate side-chains 216 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 GLN C 786 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044345 restraints weight = 101447.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045711 restraints weight = 54424.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046448 restraints weight = 36191.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047095 restraints weight = 27744.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047578 restraints weight = 22060.659| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18493 Z= 0.114 Angle : 0.588 10.978 25030 Z= 0.293 Chirality : 0.040 0.192 2807 Planarity : 0.003 0.043 3066 Dihedral : 4.865 48.143 2539 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.91 % Allowed : 17.07 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.18), residues: 2260 helix: 2.48 (0.14), residues: 1339 sheet: -1.09 (0.40), residues: 161 loop : -1.11 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 507 TYR 0.017 0.001 TYR G 156 PHE 0.011 0.001 PHE D 437 TRP 0.011 0.001 TRP A 788 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00251 (18478) covalent geometry : angle 0.58061 (25002) SS BOND : bond 0.00515 ( 14) SS BOND : angle 2.78165 ( 28) hydrogen bonds : bond 0.03605 ( 1066) hydrogen bonds : angle 3.84647 ( 3120) Misc. bond : bond 0.00120 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8975 (mpp) cc_final: 0.8688 (mpp) REVERT: A 607 MET cc_start: 0.9404 (tpp) cc_final: 0.8633 (mmt) REVERT: A 637 SER cc_start: 0.9813 (m) cc_final: 0.9552 (p) REVERT: A 696 MET cc_start: 0.8544 (mtm) cc_final: 0.8290 (mtm) REVERT: A 743 MET cc_start: 0.9375 (ppp) cc_final: 0.9057 (ppp) REVERT: B 423 MET cc_start: 0.8691 (mmt) cc_final: 0.8288 (mmm) REVERT: B 436 MET cc_start: 0.9258 (ptp) cc_final: 0.8680 (ppp) REVERT: B 485 MET cc_start: 0.8357 (mmm) cc_final: 0.8130 (mmm) REVERT: B 518 MET cc_start: 0.7830 (mmm) cc_final: 0.7511 (mmm) REVERT: B 607 MET cc_start: 0.9312 (ttm) cc_final: 0.9032 (mtt) REVERT: B 608 GLN cc_start: 0.9468 (mm110) cc_final: 0.9255 (mm-40) REVERT: B 631 THR cc_start: 0.9447 (m) cc_final: 0.9119 (m) REVERT: B 730 MET cc_start: 0.9086 (tpt) cc_final: 0.8402 (mmm) REVERT: C 423 MET cc_start: 0.7881 (tpp) cc_final: 0.7566 (tpp) REVERT: C 429 MET cc_start: 0.8264 (mpp) cc_final: 0.7892 (mpp) REVERT: C 515 LYS cc_start: 0.8945 (mptt) cc_final: 0.8448 (tttt) REVERT: D 518 MET cc_start: 0.8700 (ptm) cc_final: 0.8301 (ppp) REVERT: D 607 MET cc_start: 0.9284 (mmt) cc_final: 0.8761 (mmm) REVERT: D 608 GLN cc_start: 0.9195 (mp10) cc_final: 0.8923 (mp10) REVERT: D 730 MET cc_start: 0.8880 (mmm) cc_final: 0.8592 (mmm) REVERT: E 191 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9215 (mm-30) REVERT: E 200 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: F 24 MET cc_start: 0.9600 (mmm) cc_final: 0.9287 (tpp) REVERT: F 33 TRP cc_start: 0.8910 (m100) cc_final: 0.8531 (m100) REVERT: F 117 MET cc_start: 0.8268 (tpt) cc_final: 0.7973 (tpt) REVERT: F 176 TYR cc_start: 0.8916 (m-80) cc_final: 0.8707 (m-80) REVERT: G 33 TRP cc_start: 0.9075 (m100) cc_final: 0.8556 (m100) REVERT: G 117 MET cc_start: 0.8378 (tpp) cc_final: 0.7959 (tpp) REVERT: H 10 MET cc_start: 0.9047 (mmm) cc_final: 0.8525 (tpp) REVERT: H 207 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8957 (mm-40) outliers start: 36 outliers final: 24 residues processed: 225 average time/residue: 0.1258 time to fit residues: 44.7222 Evaluate side-chains 213 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 37 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 786 ASN D 433 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.059078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041274 restraints weight = 104447.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042542 restraints weight = 55878.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043372 restraints weight = 36413.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043941 restraints weight = 27290.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044265 restraints weight = 22194.911| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18493 Z= 0.286 Angle : 0.696 13.350 25030 Z= 0.359 Chirality : 0.042 0.195 2807 Planarity : 0.004 0.068 3066 Dihedral : 4.916 40.886 2539 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 2.34 % Allowed : 17.76 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.18), residues: 2260 helix: 2.32 (0.14), residues: 1333 sheet: -1.27 (0.40), residues: 172 loop : -1.12 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 697 TYR 0.020 0.001 TYR G 156 PHE 0.017 0.002 PHE D 563 TRP 0.016 0.002 TRP A 482 HIS 0.006 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00596 (18478) covalent geometry : angle 0.69266 (25002) SS BOND : bond 0.00543 ( 14) SS BOND : angle 2.23151 ( 28) hydrogen bonds : bond 0.04082 ( 1066) hydrogen bonds : angle 4.33783 ( 3120) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.9102 (mpp) cc_final: 0.8825 (mpp) REVERT: A 518 MET cc_start: 0.8844 (ttm) cc_final: 0.8602 (mtt) REVERT: A 525 MET cc_start: 0.8672 (ppp) cc_final: 0.8265 (ppp) REVERT: A 607 MET cc_start: 0.9464 (tpp) cc_final: 0.8658 (mmt) REVERT: A 637 SER cc_start: 0.9832 (m) cc_final: 0.9611 (p) REVERT: A 696 MET cc_start: 0.8587 (mtm) cc_final: 0.8276 (mtm) REVERT: A 743 MET cc_start: 0.9422 (ppp) cc_final: 0.9074 (ppp) REVERT: B 423 MET cc_start: 0.8803 (mmt) cc_final: 0.8410 (mmm) REVERT: B 436 MET cc_start: 0.9292 (ptp) cc_final: 0.8816 (ppp) REVERT: B 485 MET cc_start: 0.8378 (mmm) cc_final: 0.8163 (mmm) REVERT: B 518 MET cc_start: 0.8180 (mmm) cc_final: 0.7849 (mmm) REVERT: B 607 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9040 (mtt) REVERT: B 631 THR cc_start: 0.9501 (m) cc_final: 0.9131 (p) REVERT: B 730 MET cc_start: 0.9194 (tpt) cc_final: 0.8571 (mmm) REVERT: C 423 MET cc_start: 0.8018 (tpp) cc_final: 0.7730 (tpp) REVERT: D 518 MET cc_start: 0.8636 (ptm) cc_final: 0.8213 (ppp) REVERT: D 607 MET cc_start: 0.9311 (mmt) cc_final: 0.8716 (mmm) REVERT: D 608 GLN cc_start: 0.9307 (mp10) cc_final: 0.8896 (mp10) REVERT: F 24 MET cc_start: 0.9666 (mmm) cc_final: 0.9138 (tpp) REVERT: F 33 TRP cc_start: 0.9066 (m100) cc_final: 0.8600 (m100) REVERT: F 117 MET cc_start: 0.8347 (tpt) cc_final: 0.8058 (tpt) REVERT: G 117 MET cc_start: 0.8514 (tpp) cc_final: 0.8106 (tpp) REVERT: G 203 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.9127 (m-30) REVERT: G 206 LYS cc_start: 0.9361 (mtmt) cc_final: 0.8917 (mtmm) outliers start: 44 outliers final: 34 residues processed: 212 average time/residue: 0.1210 time to fit residues: 40.8982 Evaluate side-chains 213 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042966 restraints weight = 101356.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044306 restraints weight = 53773.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045203 restraints weight = 34898.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045716 restraints weight = 25775.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046101 restraints weight = 21103.853| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18493 Z= 0.121 Angle : 0.621 12.616 25030 Z= 0.308 Chirality : 0.041 0.191 2807 Planarity : 0.003 0.042 3066 Dihedral : 4.853 39.908 2539 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.70 % Allowed : 18.77 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 2260 helix: 2.50 (0.14), residues: 1331 sheet: -0.81 (0.41), residues: 167 loop : -1.13 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 706 TYR 0.018 0.001 TYR G 156 PHE 0.015 0.001 PHE D 553 TRP 0.012 0.001 TRP A 788 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00269 (18478) covalent geometry : angle 0.61800 (25002) SS BOND : bond 0.00384 ( 14) SS BOND : angle 1.97209 ( 28) hydrogen bonds : bond 0.03807 ( 1066) hydrogen bonds : angle 4.00712 ( 3120) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.9058 (mpp) cc_final: 0.8776 (mpp) REVERT: A 525 MET cc_start: 0.8650 (ppp) cc_final: 0.8319 (ppp) REVERT: A 607 MET cc_start: 0.9398 (tpp) cc_final: 0.8601 (mmt) REVERT: A 609 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7520 (tp40) REVERT: A 637 SER cc_start: 0.9826 (m) cc_final: 0.9582 (p) REVERT: A 696 MET cc_start: 0.8522 (mtm) cc_final: 0.8288 (mtm) REVERT: A 727 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8931 (mp0) REVERT: A 743 MET cc_start: 0.9419 (ppp) cc_final: 0.9109 (ppp) REVERT: A 819 TYR cc_start: 0.8758 (m-80) cc_final: 0.8526 (m-80) REVERT: B 423 MET cc_start: 0.8784 (mmt) cc_final: 0.8392 (mmm) REVERT: B 436 MET cc_start: 0.9317 (ptp) cc_final: 0.8872 (ppp) REVERT: B 485 MET cc_start: 0.8397 (mmm) cc_final: 0.8168 (mmm) REVERT: B 518 MET cc_start: 0.8088 (mmm) cc_final: 0.7741 (mmm) REVERT: B 607 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9069 (mtt) REVERT: B 649 GLU cc_start: 0.9266 (mm-30) cc_final: 0.9054 (mm-30) REVERT: B 730 MET cc_start: 0.9115 (tpt) cc_final: 0.8594 (mmm) REVERT: C 423 MET cc_start: 0.7932 (tpp) cc_final: 0.7623 (tpp) REVERT: C 429 MET cc_start: 0.8299 (mpp) cc_final: 0.7873 (mpp) REVERT: D 518 MET cc_start: 0.8698 (ptm) cc_final: 0.8302 (ppp) REVERT: D 607 MET cc_start: 0.9293 (mmt) cc_final: 0.8732 (mmm) REVERT: D 608 GLN cc_start: 0.9293 (mp10) cc_final: 0.8896 (mp10) REVERT: D 730 MET cc_start: 0.8919 (mmm) cc_final: 0.8568 (mmm) REVERT: E 191 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9231 (mm-30) REVERT: F 24 MET cc_start: 0.9633 (mmm) cc_final: 0.9320 (tpp) REVERT: F 33 TRP cc_start: 0.8952 (m100) cc_final: 0.8559 (m100) REVERT: F 117 MET cc_start: 0.8301 (tpt) cc_final: 0.8008 (tpt) REVERT: G 117 MET cc_start: 0.8446 (tpp) cc_final: 0.8041 (tpp) REVERT: H 10 MET cc_start: 0.9141 (mmm) cc_final: 0.8634 (tpp) outliers start: 32 outliers final: 25 residues processed: 219 average time/residue: 0.1194 time to fit residues: 41.6003 Evaluate side-chains 212 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 207 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 222 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042910 restraints weight = 101140.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044221 restraints weight = 54110.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045050 restraints weight = 35299.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045634 restraints weight = 26418.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046047 restraints weight = 21447.471| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18493 Z= 0.143 Angle : 0.654 12.319 25030 Z= 0.323 Chirality : 0.041 0.232 2807 Planarity : 0.004 0.043 3066 Dihedral : 4.785 39.769 2539 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 1.59 % Allowed : 19.19 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2260 helix: 2.51 (0.14), residues: 1328 sheet: -0.94 (0.40), residues: 178 loop : -1.06 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 697 TYR 0.020 0.001 TYR G 156 PHE 0.019 0.001 PHE C 681 TRP 0.010 0.001 TRP D 693 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00317 (18478) covalent geometry : angle 0.65179 (25002) SS BOND : bond 0.00351 ( 14) SS BOND : angle 1.78737 ( 28) hydrogen bonds : bond 0.03731 ( 1066) hydrogen bonds : angle 4.05255 ( 3120) Misc. bond : bond 0.00104 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.9041 (mpp) cc_final: 0.8763 (mpp) REVERT: A 525 MET cc_start: 0.8665 (ppp) cc_final: 0.8311 (ppp) REVERT: A 607 MET cc_start: 0.9421 (tpp) cc_final: 0.8656 (mmt) REVERT: A 609 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7512 (tp40) REVERT: A 637 SER cc_start: 0.9829 (m) cc_final: 0.9580 (p) REVERT: A 696 MET cc_start: 0.8557 (mtm) cc_final: 0.8284 (mtm) REVERT: A 727 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8942 (mp0) REVERT: A 743 MET cc_start: 0.9414 (ppp) cc_final: 0.9105 (ppp) REVERT: B 423 MET cc_start: 0.8764 (mmt) cc_final: 0.8364 (mmm) REVERT: B 436 MET cc_start: 0.9309 (ptp) cc_final: 0.8854 (ppp) REVERT: B 485 MET cc_start: 0.8408 (mmm) cc_final: 0.8178 (mmm) REVERT: B 518 MET cc_start: 0.8089 (mmm) cc_final: 0.7737 (mmm) REVERT: B 607 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9049 (mtt) REVERT: B 730 MET cc_start: 0.9105 (tpt) cc_final: 0.8448 (mmm) REVERT: C 423 MET cc_start: 0.7910 (tpp) cc_final: 0.7597 (tpp) REVERT: C 429 MET cc_start: 0.8291 (mpp) cc_final: 0.7852 (mpp) REVERT: D 518 MET cc_start: 0.8746 (ptm) cc_final: 0.8312 (ppp) REVERT: D 607 MET cc_start: 0.9327 (mmt) cc_final: 0.8765 (mmm) REVERT: D 608 GLN cc_start: 0.9333 (mp10) cc_final: 0.8926 (mp10) REVERT: D 730 MET cc_start: 0.8896 (mmm) cc_final: 0.8611 (mmm) REVERT: E 191 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9240 (mm-30) REVERT: F 24 MET cc_start: 0.9645 (mmm) cc_final: 0.9318 (tpp) REVERT: F 33 TRP cc_start: 0.8960 (m100) cc_final: 0.8609 (m100) REVERT: F 117 MET cc_start: 0.8323 (tpt) cc_final: 0.8034 (tpt) REVERT: G 117 MET cc_start: 0.8426 (tpp) cc_final: 0.8023 (tpp) REVERT: H 10 MET cc_start: 0.9141 (mmm) cc_final: 0.8643 (tpp) outliers start: 30 outliers final: 26 residues processed: 210 average time/residue: 0.1186 time to fit residues: 39.5300 Evaluate side-chains 206 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 31 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 6 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 overall best weight: 2.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.060422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042769 restraints weight = 102548.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.044076 restraints weight = 54745.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044937 restraints weight = 35633.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045503 restraints weight = 26502.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045866 restraints weight = 21540.226| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18493 Z= 0.156 Angle : 0.655 12.164 25030 Z= 0.326 Chirality : 0.041 0.211 2807 Planarity : 0.004 0.042 3066 Dihedral : 4.770 39.894 2539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.59 % Allowed : 19.25 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2260 helix: 2.52 (0.14), residues: 1323 sheet: -0.71 (0.41), residues: 152 loop : -1.14 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 697 TYR 0.021 0.001 TYR G 156 PHE 0.032 0.001 PHE H 18 TRP 0.008 0.001 TRP A 788 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00344 (18478) covalent geometry : angle 0.65305 (25002) SS BOND : bond 0.00391 ( 14) SS BOND : angle 1.74177 ( 28) hydrogen bonds : bond 0.03714 ( 1066) hydrogen bonds : angle 4.07690 ( 3120) Misc. bond : bond 0.00096 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.07 seconds wall clock time: 53 minutes 46.46 seconds (3226.46 seconds total)