Starting phenix.real_space_refine on Wed Mar 4 05:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.map" model { file = "/net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n8f_49127/03_2026/9n8f_49127.cif" } resolution = 3.13 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= 0.000 sd= 0.026 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 51 5.16 5 C 6984 2.51 5 N 1875 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11001 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1184 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 12, 'TRANS': 142} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 882 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 770 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "I" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 882 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 770 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1184 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 12, 'TRANS': 142} Chain: "F" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "J" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 882 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 770 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1184 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 12, 'TRANS': 142} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.42, per 1000 atoms: 0.22 Number of scatterers: 11001 At special positions: 0 Unit cell: (148.463, 147.574, 90.678, 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 51 16.00 O 2091 8.00 N 1875 7.00 C 6984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS D 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " 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=0, symmetry=0 Links applied BETA1-4 " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 40 " " NAG B 601 " - " ASN B 40 " " NAG C 601 " - " ASN C 40 " " NAG R 1 " - " ASN D 563 " " NAG S 1 " - " ASN E 563 " " NAG T 1 " - " ASN F 563 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 453.0 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 31 sheets defined 14.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.881A pdb=" N GLY A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.512A pdb=" N ASN D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 570 " --> pdb=" O THR D 566 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.766A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.558A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 576 removed outlier: 3.746A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 570 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 574 " --> pdb=" O GLN E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 599 removed outlier: 3.526A pdb=" N TRP E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY E 599 " --> pdb=" O ARG E 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.877A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.649A pdb=" N GLY C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.597A pdb=" N ASN F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 570 " --> pdb=" O THR F 566 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 574 " --> pdb=" O GLN F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.721A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.809A pdb=" N GLY B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.916A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 110 removed outlier: 7.184A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 137 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 515 through 517 Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 98 through 100 removed outlier: 6.998A pdb=" N PHE H 98 " --> pdb=" O ILE H 100E" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.564A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.515A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 515 through 517 Processing sheet with id=AB3, first strand: chain 'E' and resid 580 through 581 Processing sheet with id=AB4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.644A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 89 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 98 through 100 removed outlier: 7.027A pdb=" N PHE I 98 " --> pdb=" O ILE I 100E" (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AB8, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.579A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 43 through 46 Processing sheet with id=AC1, first strand: chain 'C' and resid 43 through 46 removed outlier: 7.032A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'C' and resid 105 through 110 removed outlier: 7.159A pdb=" N GLU C 106 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR C 137 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 515 through 517 Processing sheet with id=AC5, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 56 through 59 removed outlier: 4.308A pdb=" N SER J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP J 35 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL J 89 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 56 through 59 removed outlier: 4.308A pdb=" N SER J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP J 35 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL J 89 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 98 through 100 removed outlier: 7.127A pdb=" N PHE J 98 " --> pdb=" O ILE J 100E" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 removed outlier: 6.269A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ILE N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 12.605A pdb=" N SER N 65 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.381A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AD3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AD4, first strand: chain 'B' and resid 105 through 107 removed outlier: 9.178A pdb=" N ALA B 105 " --> pdb=" O ARG B 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 391 hydrogen bonds defined for protein. 969 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: 1.26 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3555 1.34 - 1.46: 2639 1.46 - 1.58: 5014 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 11268 Sorted by residual: bond pdb=" N ASP I 95 " pdb=" CA ASP I 95 " ideal model delta sigma weight residual 1.462 1.448 0.014 9.30e-03 1.16e+04 2.32e+00 bond pdb=" CA ILE A 79 " pdb=" CB ILE A 79 " ideal model delta sigma weight residual 1.534 1.544 -0.009 6.80e-03 2.16e+04 1.82e+00 bond pdb=" CB ASN A 40 " pdb=" CG ASN A 40 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.84e-02 2.95e+03 1.61e+00 bond pdb=" C GLY L 99 " pdb=" N GLY L 100 " ideal model delta sigma weight residual 1.332 1.324 0.008 6.60e-03 2.30e+04 1.57e+00 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 15336 3.69 - 7.38: 49 7.38 - 11.07: 4 11.07 - 14.77: 0 14.77 - 18.46: 1 Bond angle restraints: 15390 Sorted by residual: angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 134.76 -18.46 3.50e+00 8.16e-02 2.78e+01 angle pdb=" C TRP J 7 " pdb=" N GLY J 8 " pdb=" CA GLY J 8 " ideal model delta sigma weight residual 121.41 131.40 -9.99 1.96e+00 2.60e-01 2.60e+01 angle pdb=" C GLU H 16 " pdb=" CA GLU H 16 " pdb=" CB GLU H 16 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 112.18 118.55 -6.37 1.34e+00 5.57e-01 2.26e+01 angle pdb=" C GLU I 16 " pdb=" CA GLU I 16 " pdb=" CB GLU I 16 " ideal model delta sigma weight residual 116.34 110.32 6.02 1.40e+00 5.10e-01 1.85e+01 ... (remaining 15385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6025 17.95 - 35.91: 540 35.91 - 53.86: 103 53.86 - 71.82: 28 71.82 - 89.77: 15 Dihedral angle restraints: 6711 sinusoidal: 2535 harmonic: 4176 Sorted by residual: dihedral pdb=" CB CYS C 53 " pdb=" SG CYS C 53 " pdb=" SG CYS F 609 " pdb=" CB CYS F 609 " ideal model delta sinusoidal sigma weight residual 93.00 9.58 83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 147 " pdb=" CB CYS B 147 " ideal model delta sinusoidal sigma weight residual 93.00 148.31 -55.31 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS D 609 " pdb=" CB CYS D 609 " ideal model delta sinusoidal sigma weight residual 93.00 138.92 -45.92 1 1.00e+01 1.00e-02 2.92e+01 ... (remaining 6708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1280 0.042 - 0.085: 333 0.085 - 0.127: 124 0.127 - 0.169: 15 0.169 - 0.211: 3 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CB THR J 99 " pdb=" CA THR J 99 " pdb=" OG1 THR J 99 " pdb=" CG2 THR J 99 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C3 NAG A 601 " pdb=" C2 NAG A 601 " pdb=" C4 NAG A 601 " pdb=" O3 NAG A 601 " both_signs ideal model delta sigma weight residual False 2.45 2.26 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 1752 not shown) Planarity restraints: 1983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 7 " 0.030 2.00e-02 2.50e+03 3.21e-02 2.57e+01 pdb=" CG TRP I 7 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP I 7 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP I 7 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP I 7 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP I 7 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 7 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 7 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 7 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 40 " 0.001 2.00e-02 2.50e+03 2.45e-02 7.53e+00 pdb=" CG ASN C 40 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 40 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 40 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 7 " 0.017 2.00e-02 2.50e+03 1.72e-02 7.37e+00 pdb=" CG TRP J 7 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP J 7 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP J 7 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 7 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 7 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP J 7 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 7 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 7 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP J 7 " 0.003 2.00e-02 2.50e+03 ... (remaining 1980 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 482 2.72 - 3.26: 10594 3.26 - 3.81: 16642 3.81 - 4.35: 20212 4.35 - 4.90: 35992 Nonbonded interactions: 83922 Sorted by model distance: nonbonded pdb=" OH TYR E 517 " pdb=" OG1 THR I 99 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR B 99 " pdb=" O TYR B 162 " model vdw 2.181 3.040 nonbonded pdb=" O LYS J 43 " pdb=" OH TYR N 87 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR M 36 " pdb=" OE1 GLN M 89 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 99 " pdb=" O TYR C 162 " model vdw 2.227 3.040 ... (remaining 83917 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.003 0.034 11298 Z= 0.162 Angle : 0.758 18.456 15459 Z= 0.418 Chirality : 0.044 0.211 1755 Planarity : 0.005 0.046 1977 Dihedral : 14.687 89.769 3990 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.67 % Allowed : 20.74 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.72 (0.22), residues: 1443 helix: -1.18 (0.45), residues: 136 sheet: -0.61 (0.24), residues: 491 loop : -1.47 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 134 TYR 0.020 0.001 TYR L 86 PHE 0.010 0.001 PHE M 62 TRP 0.086 0.002 TRP I 7 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00315 (11268) covalent geometry : angle 0.74352 (15390) SS BOND : bond 0.00255 ( 21) SS BOND : angle 0.98639 ( 42) hydrogen bonds : bond 0.16103 ( 364) hydrogen bonds : angle 7.75989 ( 969) link_BETA1-4 : bond 0.00215 ( 3) link_BETA1-4 : angle 1.64248 ( 9) link_NAG-ASN : bond 0.00541 ( 6) link_NAG-ASN : angle 4.09191 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.6915 (tp30) cc_final: 0.6678 (tt0) REVERT: A 140 LYS cc_start: 0.8172 (mttt) cc_final: 0.7907 (mptt) REVERT: A 156 ASP cc_start: 0.8279 (t0) cc_final: 0.7985 (t0) REVERT: D 550 ASN cc_start: 0.7728 (t0) cc_final: 0.7349 (t0) REVERT: D 595 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8015 (mtt90) REVERT: D 596 ARG cc_start: 0.7895 (ttt-90) cc_final: 0.7439 (ttt-90) REVERT: D 597 TRP cc_start: 0.5027 (t-100) cc_final: 0.4512 (t-100) REVERT: H 32 TYR cc_start: 0.8190 (m-80) cc_final: 0.7619 (m-80) REVERT: L 33 LEU cc_start: 0.6958 (tt) cc_final: 0.6178 (mp) REVERT: L 65 SER cc_start: 0.8162 (t) cc_final: 0.7840 (p) REVERT: E 587 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7540 (mtt-85) REVERT: E 596 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.6957 (ttt-90) REVERT: I 52 ASP cc_start: 0.7594 (t0) cc_final: 0.7307 (t0) REVERT: I 63 LEU cc_start: 0.6708 (tp) cc_final: 0.6448 (tt) REVERT: M 4 MET cc_start: 0.0235 (mtm) cc_final: -0.2976 (ttm) REVERT: M 33 LEU cc_start: 0.7013 (tt) cc_final: 0.6073 (mp) REVERT: M 59 PRO cc_start: 0.7949 (Cg_exo) cc_final: 0.7745 (Cg_endo) REVERT: C 33 MET cc_start: 0.6146 (mtm) cc_final: 0.5796 (mtm) REVERT: C 106 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8415 (mm-30) REVERT: F 550 ASN cc_start: 0.7802 (t0) cc_final: 0.7247 (m-40) REVERT: F 596 ARG cc_start: 0.7828 (ttt-90) cc_final: 0.7411 (ttt-90) REVERT: N 33 LEU cc_start: 0.6934 (tt) cc_final: 0.6107 (mp) REVERT: N 42 ARG cc_start: 0.6599 (mmm160) cc_final: 0.6334 (mmm160) REVERT: N 70 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7955 (t0) REVERT: B 44 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: B 103 GLU cc_start: 0.7913 (tt0) cc_final: 0.7420 (tt0) REVERT: B 106 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8246 (mm-30) outliers start: 18 outliers final: 14 residues processed: 193 average time/residue: 0.1176 time to fit residues: 31.0754 Evaluate side-chains 190 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain M residue 32 ASN Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN H 34 HIS L 53 ASN L 79 GLN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 586 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN F 586 ASN J 60 ASN N 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.191250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135963 restraints weight = 13223.837| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.47 r_work: 0.3723 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11298 Z= 0.142 Angle : 0.623 14.407 15459 Z= 0.312 Chirality : 0.045 0.173 1755 Planarity : 0.004 0.044 1977 Dihedral : 6.244 58.443 1792 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 3.33 % Allowed : 19.54 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1443 helix: -0.48 (0.44), residues: 141 sheet: -0.34 (0.25), residues: 461 loop : -1.50 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 595 TYR 0.018 0.002 TYR L 86 PHE 0.013 0.001 PHE F 572 TRP 0.025 0.001 TRP I 7 HIS 0.003 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00324 (11268) covalent geometry : angle 0.61241 (15390) SS BOND : bond 0.00228 ( 21) SS BOND : angle 0.82902 ( 42) hydrogen bonds : bond 0.03635 ( 364) hydrogen bonds : angle 5.69400 ( 969) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 1.65810 ( 9) link_NAG-ASN : bond 0.00212 ( 6) link_NAG-ASN : angle 3.07171 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8265 (mttt) cc_final: 0.7965 (mptt) REVERT: A 156 ASP cc_start: 0.8332 (t0) cc_final: 0.8046 (t0) REVERT: D 550 ASN cc_start: 0.7892 (t0) cc_final: 0.7381 (t0) REVERT: D 595 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7913 (mtt90) REVERT: D 596 ARG cc_start: 0.7914 (ttt-90) cc_final: 0.7540 (ttt-90) REVERT: D 597 TRP cc_start: 0.5050 (t-100) cc_final: 0.4564 (t-100) REVERT: H 32 TYR cc_start: 0.8206 (m-80) cc_final: 0.7983 (m-80) REVERT: E 587 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7554 (mtt-85) REVERT: E 596 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.7063 (ttt-90) REVERT: I 63 LEU cc_start: 0.6920 (tp) cc_final: 0.6646 (tt) REVERT: M 4 MET cc_start: 0.0540 (mtm) cc_final: -0.2749 (ttm) REVERT: M 33 LEU cc_start: 0.7103 (tt) cc_final: 0.6202 (mp) REVERT: M 59 PRO cc_start: 0.8005 (Cg_exo) cc_final: 0.7773 (Cg_endo) REVERT: C 69 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: C 137 TYR cc_start: 0.7250 (m-80) cc_final: 0.6780 (t80) REVERT: J 7 TRP cc_start: 0.6226 (m100) cc_final: 0.5951 (m100) REVERT: N 33 LEU cc_start: 0.7068 (tt) cc_final: 0.6238 (mp) REVERT: N 42 ARG cc_start: 0.6548 (mmm160) cc_final: 0.6249 (mmm160) REVERT: N 70 ASP cc_start: 0.8063 (m-30) cc_final: 0.7774 (t0) REVERT: B 44 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4856 (pm20) REVERT: B 106 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8261 (mm-30) REVERT: B 114 LYS cc_start: 0.7366 (ttpt) cc_final: 0.7127 (ttpp) outliers start: 36 outliers final: 25 residues processed: 208 average time/residue: 0.1161 time to fit residues: 33.2201 Evaluate side-chains 201 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.192888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137481 restraints weight = 13197.233| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.50 r_work: 0.3754 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11298 Z= 0.107 Angle : 0.580 15.627 15459 Z= 0.288 Chirality : 0.044 0.159 1755 Planarity : 0.004 0.042 1977 Dihedral : 5.750 58.808 1783 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.89 % Allowed : 20.28 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.26 (0.22), residues: 1443 helix: 0.47 (0.48), residues: 123 sheet: -0.32 (0.25), residues: 473 loop : -1.37 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 595 TYR 0.016 0.001 TYR L 86 PHE 0.006 0.001 PHE F 572 TRP 0.033 0.001 TRP I 7 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00238 (11268) covalent geometry : angle 0.57067 (15390) SS BOND : bond 0.00212 ( 21) SS BOND : angle 0.66833 ( 42) hydrogen bonds : bond 0.03224 ( 364) hydrogen bonds : angle 5.25004 ( 969) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 1.70561 ( 9) link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 2.83869 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7718 (tt0) cc_final: 0.7455 (mm-30) REVERT: A 50 GLN cc_start: 0.8058 (tp40) cc_final: 0.7848 (tp40) REVERT: A 140 LYS cc_start: 0.8304 (mttt) cc_final: 0.7972 (mptt) REVERT: A 156 ASP cc_start: 0.8268 (t0) cc_final: 0.7956 (t0) REVERT: D 540 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: D 595 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7889 (mtt90) REVERT: D 596 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7538 (ttt-90) REVERT: D 597 TRP cc_start: 0.5035 (t-100) cc_final: 0.4423 (t-100) REVERT: H 32 TYR cc_start: 0.8124 (m-80) cc_final: 0.7870 (m-80) REVERT: H 33 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: L 33 LEU cc_start: 0.6758 (tt) cc_final: 0.5909 (mp) REVERT: E 587 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7456 (mtt-85) REVERT: E 596 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.6958 (ttt-90) REVERT: I 7 TRP cc_start: 0.5914 (m100) cc_final: 0.5694 (m100) REVERT: I 63 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6618 (tt) REVERT: M 4 MET cc_start: 0.0589 (mtm) cc_final: -0.2606 (ttm) REVERT: M 33 LEU cc_start: 0.6967 (tt) cc_final: 0.6215 (mp) REVERT: M 59 PRO cc_start: 0.7930 (Cg_exo) cc_final: 0.7693 (Cg_endo) REVERT: C 33 MET cc_start: 0.6170 (mtm) cc_final: 0.5885 (mtm) REVERT: C 137 TYR cc_start: 0.7135 (m-80) cc_final: 0.6632 (t80) REVERT: F 540 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: F 596 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7151 (ttt-90) REVERT: J 7 TRP cc_start: 0.6138 (m100) cc_final: 0.5824 (m100) REVERT: N 33 LEU cc_start: 0.6966 (tt) cc_final: 0.6161 (mp) REVERT: N 42 ARG cc_start: 0.6562 (mmm160) cc_final: 0.6270 (mmm160) REVERT: N 70 ASP cc_start: 0.7972 (m-30) cc_final: 0.7717 (t0) REVERT: B 44 GLU cc_start: 0.5005 (pt0) cc_final: 0.4724 (pm20) REVERT: B 106 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8189 (mm-30) REVERT: B 114 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7182 (ttpp) outliers start: 42 outliers final: 30 residues processed: 217 average time/residue: 0.1097 time to fit residues: 32.9607 Evaluate side-chains 214 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN N 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.182098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126904 restraints weight = 13732.385| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.51 r_work: 0.3516 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11298 Z= 0.261 Angle : 0.732 14.472 15459 Z= 0.372 Chirality : 0.048 0.165 1755 Planarity : 0.005 0.045 1977 Dihedral : 6.556 59.086 1778 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.87 % Favored : 90.92 % Rotamer: Outliers : 5.83 % Allowed : 20.00 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.73 (0.22), residues: 1443 helix: -0.74 (0.42), residues: 141 sheet: -0.32 (0.25), residues: 445 loop : -1.73 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 595 TYR 0.022 0.002 TYR L 86 PHE 0.022 0.003 PHE F 572 TRP 0.034 0.002 TRP E 518 HIS 0.006 0.002 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00621 (11268) covalent geometry : angle 0.72014 (15390) SS BOND : bond 0.00380 ( 21) SS BOND : angle 1.46327 ( 42) hydrogen bonds : bond 0.04226 ( 364) hydrogen bonds : angle 5.56107 ( 969) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 2.10337 ( 9) link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 3.13149 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8404 (mttt) cc_final: 0.8182 (mttm) REVERT: A 156 ASP cc_start: 0.8543 (t0) cc_final: 0.8320 (t0) REVERT: D 552 ASN cc_start: 0.8406 (m110) cc_final: 0.8072 (m110) REVERT: D 554 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6527 (mp) REVERT: D 596 ARG cc_start: 0.7877 (ttt-90) cc_final: 0.7627 (ttt-90) REVERT: D 597 TRP cc_start: 0.5220 (t-100) cc_final: 0.4470 (t-100) REVERT: H 32 TYR cc_start: 0.8266 (m-80) cc_final: 0.7946 (m-80) REVERT: L 33 LEU cc_start: 0.6871 (tt) cc_final: 0.5867 (mp) REVERT: E 554 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6336 (tt) REVERT: E 587 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7550 (mtt-85) REVERT: E 596 ARG cc_start: 0.8082 (ttt-90) cc_final: 0.7021 (ttt-90) REVERT: I 100 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.6429 (m-90) REVERT: M 4 MET cc_start: 0.0631 (mtm) cc_final: -0.3259 (ttp) REVERT: M 33 LEU cc_start: 0.7113 (tt) cc_final: 0.6248 (mp) REVERT: M 97 THR cc_start: 0.4140 (OUTLIER) cc_final: 0.3669 (m) REVERT: C 100 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7031 (pt0) REVERT: C 137 TYR cc_start: 0.7293 (m-80) cc_final: 0.6610 (t80) REVERT: F 550 ASN cc_start: 0.8012 (t0) cc_final: 0.7355 (m-40) REVERT: F 596 ARG cc_start: 0.7765 (ttt-90) cc_final: 0.7055 (ttt-90) REVERT: N 42 ARG cc_start: 0.6394 (mmm160) cc_final: 0.6050 (mmm160) REVERT: N 70 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7511 (t0) REVERT: B 114 LYS cc_start: 0.7566 (ttpt) cc_final: 0.7308 (ttpp) REVERT: B 156 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0) outliers start: 63 outliers final: 41 residues processed: 241 average time/residue: 0.1035 time to fit residues: 35.0117 Evaluate side-chains 242 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 65 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 549 HIS ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.184366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.128717 restraints weight = 13511.070| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.49 r_work: 0.3634 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11298 Z= 0.160 Angle : 0.640 15.210 15459 Z= 0.321 Chirality : 0.046 0.159 1755 Planarity : 0.004 0.041 1977 Dihedral : 6.117 55.154 1778 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.24 % Favored : 93.56 % Rotamer: Outliers : 4.63 % Allowed : 21.76 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.58 (0.22), residues: 1443 helix: -0.12 (0.47), residues: 123 sheet: -0.40 (0.26), residues: 437 loop : -1.58 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.017 0.002 TYR M 86 PHE 0.013 0.002 PHE D 572 TRP 0.028 0.002 TRP E 518 HIS 0.003 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00375 (11268) covalent geometry : angle 0.62977 (15390) SS BOND : bond 0.00286 ( 21) SS BOND : angle 1.13720 ( 42) hydrogen bonds : bond 0.03442 ( 364) hydrogen bonds : angle 5.26637 ( 969) link_BETA1-4 : bond 0.00125 ( 3) link_BETA1-4 : angle 2.00799 ( 9) link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 2.80626 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8391 (mttt) cc_final: 0.8153 (mttm) REVERT: A 156 ASP cc_start: 0.8419 (t0) cc_final: 0.8133 (t0) REVERT: D 552 ASN cc_start: 0.8312 (m110) cc_final: 0.8007 (m110) REVERT: D 596 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7231 (ttt-90) REVERT: D 597 TRP cc_start: 0.5077 (t-100) cc_final: 0.4157 (t-100) REVERT: H 32 TYR cc_start: 0.8175 (m-80) cc_final: 0.7805 (m-80) REVERT: L 30 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7720 (p) REVERT: L 33 LEU cc_start: 0.6806 (tt) cc_final: 0.5832 (mp) REVERT: E 554 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6160 (tp) REVERT: E 587 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7438 (mtt-85) REVERT: E 596 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.6975 (ttt-90) REVERT: I 7 TRP cc_start: 0.5943 (m100) cc_final: 0.5594 (m100) REVERT: M 4 MET cc_start: 0.0492 (mtm) cc_final: -0.3017 (ttp) REVERT: M 33 LEU cc_start: 0.7014 (tt) cc_final: 0.6183 (mp) REVERT: C 100 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: C 137 TYR cc_start: 0.7250 (m-80) cc_final: 0.6568 (t80) REVERT: F 540 GLU cc_start: 0.6970 (pm20) cc_final: 0.6595 (mp0) REVERT: F 596 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.6962 (ttt-90) REVERT: F 597 TRP cc_start: 0.5095 (t-100) cc_final: 0.4388 (t-100) REVERT: J 6 GLU cc_start: 0.3687 (mt-10) cc_final: 0.3020 (mt-10) REVERT: J 7 TRP cc_start: 0.5973 (m100) cc_final: 0.5623 (m100) REVERT: N 33 LEU cc_start: 0.6527 (tt) cc_final: 0.5588 (mp) REVERT: N 70 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7482 (t0) REVERT: B 44 GLU cc_start: 0.4833 (OUTLIER) cc_final: 0.4482 (pm20) REVERT: B 114 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7304 (ttpp) outliers start: 50 outliers final: 39 residues processed: 226 average time/residue: 0.1066 time to fit residues: 34.1021 Evaluate side-chains 226 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127869 restraints weight = 13495.889| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.45 r_work: 0.3624 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11298 Z= 0.176 Angle : 0.653 15.569 15459 Z= 0.325 Chirality : 0.046 0.162 1755 Planarity : 0.004 0.041 1977 Dihedral : 6.037 54.675 1778 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.83 % Favored : 91.96 % Rotamer: Outliers : 5.46 % Allowed : 21.30 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.62 (0.22), residues: 1443 helix: -0.46 (0.44), residues: 141 sheet: -0.26 (0.26), residues: 422 loop : -1.66 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 595 TYR 0.019 0.002 TYR M 86 PHE 0.014 0.002 PHE E 572 TRP 0.028 0.002 TRP E 518 HIS 0.003 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00414 (11268) covalent geometry : angle 0.64203 (15390) SS BOND : bond 0.00308 ( 21) SS BOND : angle 1.13759 ( 42) hydrogen bonds : bond 0.03510 ( 364) hydrogen bonds : angle 5.21424 ( 969) link_BETA1-4 : bond 0.00270 ( 3) link_BETA1-4 : angle 2.16327 ( 9) link_NAG-ASN : bond 0.00194 ( 6) link_NAG-ASN : angle 2.84699 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8431 (mttt) cc_final: 0.8169 (mttm) REVERT: A 156 ASP cc_start: 0.8421 (t0) cc_final: 0.8131 (t0) REVERT: D 540 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: D 547 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7895 (tt) REVERT: D 552 ASN cc_start: 0.8327 (m110) cc_final: 0.7735 (p0) REVERT: D 596 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.6724 (ttt-90) REVERT: D 597 TRP cc_start: 0.5116 (t-100) cc_final: 0.4149 (t-100) REVERT: H 32 TYR cc_start: 0.8183 (m-80) cc_final: 0.7794 (m-80) REVERT: L 33 LEU cc_start: 0.6719 (tt) cc_final: 0.5736 (mp) REVERT: E 554 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6097 (tp) REVERT: E 587 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7463 (mtt-85) REVERT: E 596 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7021 (ttt-90) REVERT: I 7 TRP cc_start: 0.6027 (m100) cc_final: 0.5627 (m100) REVERT: M 4 MET cc_start: 0.0478 (mtm) cc_final: -0.2959 (ttp) REVERT: M 33 LEU cc_start: 0.6950 (tt) cc_final: 0.5988 (mp) REVERT: M 97 THR cc_start: 0.4312 (OUTLIER) cc_final: 0.3853 (m) REVERT: C 100 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6842 (pt0) REVERT: F 540 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: F 596 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7219 (ttt-90) REVERT: F 597 TRP cc_start: 0.5097 (t-100) cc_final: 0.4109 (t-100) REVERT: J 7 TRP cc_start: 0.6022 (m100) cc_final: 0.5694 (m100) REVERT: N 33 LEU cc_start: 0.6582 (tt) cc_final: 0.5613 (mp) REVERT: N 70 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7452 (t0) REVERT: B 44 GLU cc_start: 0.4883 (OUTLIER) cc_final: 0.4549 (pm20) outliers start: 59 outliers final: 41 residues processed: 227 average time/residue: 0.1066 time to fit residues: 34.2785 Evaluate side-chains 231 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 GLN E 586 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.185002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129499 restraints weight = 13405.001| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.48 r_work: 0.3638 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11298 Z= 0.129 Angle : 0.611 15.941 15459 Z= 0.303 Chirality : 0.045 0.156 1755 Planarity : 0.004 0.030 1977 Dihedral : 5.743 55.073 1778 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.51 % Favored : 93.35 % Rotamer: Outliers : 4.81 % Allowed : 22.22 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.52 (0.22), residues: 1443 helix: -0.04 (0.48), residues: 123 sheet: -0.38 (0.26), residues: 437 loop : -1.53 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.016 0.001 TYR M 86 PHE 0.009 0.001 PHE E 572 TRP 0.025 0.001 TRP E 518 HIS 0.003 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00299 (11268) covalent geometry : angle 0.60182 (15390) SS BOND : bond 0.00252 ( 21) SS BOND : angle 0.84274 ( 42) hydrogen bonds : bond 0.03189 ( 364) hydrogen bonds : angle 5.02357 ( 969) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 2.14328 ( 9) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 2.67106 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4526 (pm20) REVERT: A 47 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 103 GLU cc_start: 0.6895 (tp30) cc_final: 0.6398 (tp30) REVERT: A 140 LYS cc_start: 0.8442 (mttt) cc_final: 0.8184 (mttm) REVERT: A 156 ASP cc_start: 0.8393 (t0) cc_final: 0.8057 (t0) REVERT: D 540 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: D 547 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7814 (tt) REVERT: D 552 ASN cc_start: 0.8269 (m110) cc_final: 0.7715 (p0) REVERT: D 596 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.6709 (ttt-90) REVERT: D 597 TRP cc_start: 0.5043 (t-100) cc_final: 0.4049 (t-100) REVERT: H 32 TYR cc_start: 0.8148 (m-80) cc_final: 0.7780 (m-80) REVERT: L 33 LEU cc_start: 0.6727 (tt) cc_final: 0.5741 (mp) REVERT: E 554 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6208 (tp) REVERT: E 587 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7432 (mtt-85) REVERT: E 596 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7013 (ttt-90) REVERT: E 597 TRP cc_start: 0.4520 (t-100) cc_final: 0.4210 (t-100) REVERT: I 7 TRP cc_start: 0.6029 (m100) cc_final: 0.5577 (m100) REVERT: M 4 MET cc_start: 0.0572 (mtm) cc_final: -0.2871 (ttp) REVERT: M 33 LEU cc_start: 0.6930 (tt) cc_final: 0.5961 (mp) REVERT: C 56 HIS cc_start: 0.6914 (m90) cc_final: 0.6155 (m90) REVERT: C 100 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: F 540 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: F 596 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7192 (ttt-90) REVERT: F 597 TRP cc_start: 0.4983 (t-100) cc_final: 0.4030 (t-100) REVERT: J 7 TRP cc_start: 0.5988 (m100) cc_final: 0.5636 (m100) REVERT: N 33 LEU cc_start: 0.6646 (tt) cc_final: 0.5677 (mp) REVERT: N 70 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7361 (t0) REVERT: B 44 GLU cc_start: 0.4823 (OUTLIER) cc_final: 0.4504 (pm20) REVERT: B 79 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6634 (tt) outliers start: 52 outliers final: 37 residues processed: 228 average time/residue: 0.1046 time to fit residues: 33.8742 Evaluate side-chains 235 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.183990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128307 restraints weight = 13464.257| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.49 r_work: 0.3637 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11298 Z= 0.145 Angle : 0.631 21.123 15459 Z= 0.308 Chirality : 0.045 0.158 1755 Planarity : 0.004 0.031 1977 Dihedral : 5.674 54.843 1778 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.55 % Favored : 92.31 % Rotamer: Outliers : 4.91 % Allowed : 22.69 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.49 (0.22), residues: 1443 helix: 0.04 (0.48), residues: 123 sheet: -0.37 (0.26), residues: 437 loop : -1.52 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.016 0.001 TYR N 86 PHE 0.012 0.001 PHE E 572 TRP 0.025 0.001 TRP E 518 HIS 0.002 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00341 (11268) covalent geometry : angle 0.62204 (15390) SS BOND : bond 0.00290 ( 21) SS BOND : angle 0.87301 ( 42) hydrogen bonds : bond 0.03253 ( 364) hydrogen bonds : angle 4.98064 ( 969) link_BETA1-4 : bond 0.00237 ( 3) link_BETA1-4 : angle 2.18885 ( 9) link_NAG-ASN : bond 0.00177 ( 6) link_NAG-ASN : angle 2.67100 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4596 (pm20) REVERT: A 47 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 103 GLU cc_start: 0.6974 (tp30) cc_final: 0.6404 (tp30) REVERT: A 140 LYS cc_start: 0.8393 (mttt) cc_final: 0.8137 (mttm) REVERT: A 156 ASP cc_start: 0.8397 (t0) cc_final: 0.8057 (t0) REVERT: D 540 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: D 552 ASN cc_start: 0.8302 (m110) cc_final: 0.7794 (p0) REVERT: D 596 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.6731 (ttt-90) REVERT: D 597 TRP cc_start: 0.5069 (t-100) cc_final: 0.4092 (t-100) REVERT: H 32 TYR cc_start: 0.8165 (m-80) cc_final: 0.7792 (m-80) REVERT: L 31 ASN cc_start: 0.7795 (p0) cc_final: 0.7455 (p0) REVERT: L 33 LEU cc_start: 0.6719 (tt) cc_final: 0.5696 (mp) REVERT: E 540 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: E 554 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6249 (tp) REVERT: E 587 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7424 (mtt-85) REVERT: E 596 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.6960 (ttt-90) REVERT: E 597 TRP cc_start: 0.4528 (t-100) cc_final: 0.4211 (t-100) REVERT: I 7 TRP cc_start: 0.6040 (m100) cc_final: 0.5569 (m100) REVERT: I 52 ASP cc_start: 0.7663 (t0) cc_final: 0.7182 (t0) REVERT: M 4 MET cc_start: 0.0514 (mtm) cc_final: -0.3424 (tmm) REVERT: M 33 LEU cc_start: 0.6964 (tt) cc_final: 0.5940 (mp) REVERT: C 56 HIS cc_start: 0.6887 (m90) cc_final: 0.6640 (m90) REVERT: C 100 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6831 (pt0) REVERT: F 540 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: F 596 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.7146 (ttt-90) REVERT: F 597 TRP cc_start: 0.5010 (t-100) cc_final: 0.4056 (t-100) REVERT: J 7 TRP cc_start: 0.5938 (m100) cc_final: 0.5617 (m100) REVERT: N 33 LEU cc_start: 0.6737 (tt) cc_final: 0.5781 (mp) REVERT: N 42 ARG cc_start: 0.6662 (mmm160) cc_final: 0.6276 (mmm160) REVERT: N 70 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7313 (t0) REVERT: B 44 GLU cc_start: 0.4882 (OUTLIER) cc_final: 0.4551 (pm20) REVERT: B 79 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6672 (tt) outliers start: 53 outliers final: 37 residues processed: 223 average time/residue: 0.1013 time to fit residues: 32.2239 Evaluate side-chains 233 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 110 optimal weight: 0.0070 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.186845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131048 restraints weight = 13241.930| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.50 r_work: 0.3664 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11298 Z= 0.104 Angle : 0.588 15.887 15459 Z= 0.289 Chirality : 0.044 0.160 1755 Planarity : 0.004 0.030 1977 Dihedral : 5.391 55.347 1778 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 4.35 % Allowed : 23.06 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.47 (0.23), residues: 1443 helix: 0.32 (0.48), residues: 123 sheet: -0.68 (0.23), residues: 527 loop : -1.39 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.016 0.001 TYR M 86 PHE 0.007 0.001 PHE E 572 TRP 0.023 0.001 TRP E 518 HIS 0.002 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00237 (11268) covalent geometry : angle 0.58012 (15390) SS BOND : bond 0.00241 ( 21) SS BOND : angle 0.67006 ( 42) hydrogen bonds : bond 0.02992 ( 364) hydrogen bonds : angle 4.83263 ( 969) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 2.13123 ( 9) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 2.50104 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 137 TYR cc_start: 0.6910 (m-80) cc_final: 0.6260 (t80) REVERT: A 140 LYS cc_start: 0.8405 (mttt) cc_final: 0.8153 (mttm) REVERT: A 156 ASP cc_start: 0.8304 (t0) cc_final: 0.7955 (t0) REVERT: D 540 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: D 552 ASN cc_start: 0.8241 (m110) cc_final: 0.7727 (p0) REVERT: D 595 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7883 (mtt90) REVERT: D 596 ARG cc_start: 0.7822 (ttt-90) cc_final: 0.6895 (ttt-90) REVERT: D 597 TRP cc_start: 0.5000 (t-100) cc_final: 0.4005 (t-100) REVERT: H 32 TYR cc_start: 0.8137 (m-80) cc_final: 0.7767 (m-80) REVERT: E 540 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: E 554 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6232 (tt) REVERT: E 587 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7429 (mtt-85) REVERT: E 596 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.6983 (ttt-90) REVERT: I 7 TRP cc_start: 0.5958 (m100) cc_final: 0.5499 (m100) REVERT: I 52 ASP cc_start: 0.7635 (t0) cc_final: 0.7092 (t0) REVERT: M 4 MET cc_start: 0.0641 (mtm) cc_final: -0.3136 (ttp) REVERT: C 56 HIS cc_start: 0.6919 (m90) cc_final: 0.6689 (m90) REVERT: C 100 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: C 137 TYR cc_start: 0.7160 (m-80) cc_final: 0.6551 (t80) REVERT: F 540 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: F 595 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7390 (mtt90) REVERT: F 597 TRP cc_start: 0.4931 (t-100) cc_final: 0.4037 (t-100) REVERT: J 7 TRP cc_start: 0.6077 (m100) cc_final: 0.5775 (m100) REVERT: N 20 THR cc_start: 0.6565 (OUTLIER) cc_final: 0.6245 (t) REVERT: N 33 LEU cc_start: 0.6715 (tt) cc_final: 0.5748 (mp) REVERT: N 70 ASP cc_start: 0.7599 (m-30) cc_final: 0.7195 (t0) REVERT: B 44 GLU cc_start: 0.4863 (OUTLIER) cc_final: 0.4549 (pm20) REVERT: B 79 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6687 (tt) outliers start: 47 outliers final: 34 residues processed: 224 average time/residue: 0.1031 time to fit residues: 32.4971 Evaluate side-chains 229 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 94 optimal weight: 0.0020 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.188952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133843 restraints weight = 13320.234| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.43 r_work: 0.3729 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11298 Z= 0.101 Angle : 0.596 19.454 15459 Z= 0.288 Chirality : 0.044 0.163 1755 Planarity : 0.004 0.032 1977 Dihedral : 5.140 55.357 1777 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.80 % Allowed : 23.89 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.35 (0.23), residues: 1443 helix: 0.63 (0.48), residues: 123 sheet: -0.63 (0.23), residues: 527 loop : -1.31 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 595 TYR 0.012 0.001 TYR M 86 PHE 0.007 0.001 PHE E 572 TRP 0.024 0.001 TRP E 518 HIS 0.003 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00230 (11268) covalent geometry : angle 0.58824 (15390) SS BOND : bond 0.00326 ( 21) SS BOND : angle 0.59531 ( 42) hydrogen bonds : bond 0.02898 ( 364) hydrogen bonds : angle 4.72846 ( 969) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 2.07353 ( 9) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 2.43343 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.6946 (m-80) cc_final: 0.6465 (t80) REVERT: A 140 LYS cc_start: 0.8341 (mttt) cc_final: 0.8128 (mttm) REVERT: A 156 ASP cc_start: 0.8317 (t0) cc_final: 0.7995 (t0) REVERT: D 540 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: D 552 ASN cc_start: 0.8299 (m110) cc_final: 0.7859 (p0) REVERT: D 591 ASP cc_start: 0.8143 (m-30) cc_final: 0.7737 (m-30) REVERT: D 595 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8000 (mtt90) REVERT: D 596 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7411 (ttt-90) REVERT: D 597 TRP cc_start: 0.5070 (t-100) cc_final: 0.4098 (t-100) REVERT: H 32 TYR cc_start: 0.8250 (m-80) cc_final: 0.7943 (m-80) REVERT: L 33 LEU cc_start: 0.6776 (tt) cc_final: 0.5707 (mp) REVERT: E 540 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: E 554 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6513 (tp) REVERT: E 587 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7534 (mtt-85) REVERT: E 596 ARG cc_start: 0.8070 (ttt-90) cc_final: 0.7035 (ttt-90) REVERT: I 7 TRP cc_start: 0.5957 (m100) cc_final: 0.5575 (m100) REVERT: I 52 ASP cc_start: 0.7763 (t0) cc_final: 0.7337 (t0) REVERT: M 4 MET cc_start: 0.0897 (mtm) cc_final: -0.3079 (ttp) REVERT: M 33 LEU cc_start: 0.6919 (tt) cc_final: 0.6024 (mp) REVERT: C 56 HIS cc_start: 0.6917 (m90) cc_final: 0.6689 (m90) REVERT: C 100 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6698 (pt0) REVERT: C 137 TYR cc_start: 0.7303 (m-80) cc_final: 0.6837 (t80) REVERT: F 540 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: F 595 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7620 (mtt90) REVERT: F 596 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7297 (ttt-90) REVERT: F 597 TRP cc_start: 0.4999 (t-100) cc_final: 0.4497 (t-100) REVERT: N 33 LEU cc_start: 0.6928 (tt) cc_final: 0.5936 (mp) REVERT: N 70 ASP cc_start: 0.7592 (m-30) cc_final: 0.7211 (t0) REVERT: B 44 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.4792 (pm20) REVERT: B 79 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6969 (tt) outliers start: 41 outliers final: 29 residues processed: 215 average time/residue: 0.1067 time to fit residues: 32.2230 Evaluate side-chains 221 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 552 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.185344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130072 restraints weight = 13425.936| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.43 r_work: 0.3664 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11298 Z= 0.149 Angle : 0.627 15.798 15459 Z= 0.307 Chirality : 0.045 0.180 1755 Planarity : 0.004 0.030 1977 Dihedral : 5.306 54.648 1774 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 3.80 % Allowed : 23.80 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.49 (0.23), residues: 1443 helix: 0.49 (0.48), residues: 123 sheet: -0.70 (0.23), residues: 527 loop : -1.42 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 595 TYR 0.015 0.001 TYR L 86 PHE 0.013 0.001 PHE E 572 TRP 0.023 0.001 TRP F 518 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00350 (11268) covalent geometry : angle 0.61828 (15390) SS BOND : bond 0.00281 ( 21) SS BOND : angle 0.83243 ( 42) hydrogen bonds : bond 0.03258 ( 364) hydrogen bonds : angle 4.82029 ( 969) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 2.21521 ( 9) link_NAG-ASN : bond 0.00188 ( 6) link_NAG-ASN : angle 2.53172 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.38 seconds wall clock time: 61 minutes 52.46 seconds (3712.46 seconds total)