Starting phenix.real_space_refine on Wed Apr 10 17:10:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhg_9114/04_2024/6mhg_9114.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.221 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 66 5.16 5 C 12511 2.51 5 N 3442 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19931 Number of models: 1 Model: "" Number of chains: 23 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 10.38, per 1000 atoms: 0.52 Number of scatterers: 19931 At special positions: 0 Unit cell: (134.93, 118.45, 160.68, 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 66 16.00 O 3912 8.00 N 3442 7.00 C 12511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.10 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.08 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.16 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.08 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.10 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=1.83 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.06 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.5 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4602 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 67 sheets defined 7.6% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'W' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.934A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.384A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.469A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.469A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.677A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.276A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.429A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.429A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.997A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.862A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.629A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.629A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.156A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.156A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA C 96 " --> pdb=" O GLY C 100D" (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY C 100D" --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.634A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.634A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.425A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.425A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA D 96 " --> pdb=" O GLY D 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY D 100D" --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.558A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.558A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.436A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.436A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.556A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 84 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.556A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 84 " --> pdb=" O LEU S 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.255A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.255A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA I 96 " --> pdb=" O GLY I 100D" (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY I 100D" --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.633A pdb=" N VAL T 11 " --> pdb=" O THR T 105 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN T 37 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU T 46 " --> pdb=" O GLN T 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.633A pdb=" N VAL T 11 " --> pdb=" O THR T 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.206A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.206A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP J 101 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 9 through 13 removed outlier: 6.474A pdb=" N VAL U 11 " --> pdb=" O THR U 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 9 through 13 removed outlier: 6.474A pdb=" N VAL U 11 " --> pdb=" O THR U 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.934A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.534A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA K 96 " --> pdb=" O GLY K 100D" (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY K 100D" --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 9 through 13 removed outlier: 6.486A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 9 through 13 removed outlier: 6.486A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 19 through 24 Processing sheet with id=AG8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.701A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.241A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 9 through 13 removed outlier: 6.539A pdb=" N VAL W 11 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS W 45 " --> pdb=" O GLN W 37 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 9 through 13 removed outlier: 6.539A pdb=" N VAL W 11 " --> pdb=" O THR W 105 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 19 through 24 876 hydrogen bonds defined for protein. 1851 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: 7.31 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3292 1.30 - 1.43: 6096 1.43 - 1.56: 10900 1.56 - 1.69: 62 1.69 - 1.83: 87 Bond restraints: 20437 Sorted by residual: bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.46e+01 bond pdb=" CB HIS K 35 " pdb=" CG HIS K 35 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.01e+01 bond pdb=" CB HIS J 35 " pdb=" CG HIS J 35 " ideal model delta sigma weight residual 1.497 1.390 0.107 1.40e-02 5.10e+03 5.84e+01 bond pdb=" CB HIS G 35 " pdb=" CG HIS G 35 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.51e+01 bond pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " ideal model delta sigma weight residual 1.516 1.338 0.178 2.50e-02 1.60e+03 5.05e+01 ... (remaining 20432 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.17: 351 104.17 - 111.80: 8580 111.80 - 119.42: 8022 119.42 - 127.05: 10660 127.05 - 134.67: 235 Bond angle restraints: 27848 Sorted by residual: angle pdb=" N ARG Q 61 " pdb=" CA ARG Q 61 " pdb=" C ARG Q 61 " ideal model delta sigma weight residual 114.62 100.83 13.79 1.14e+00 7.69e-01 1.46e+02 angle pdb=" N ARG S 61 " pdb=" CA ARG S 61 " pdb=" C ARG S 61 " ideal model delta sigma weight residual 114.62 102.14 12.48 1.14e+00 7.69e-01 1.20e+02 angle pdb=" N ARG V 61 " pdb=" CA ARG V 61 " pdb=" C ARG V 61 " ideal model delta sigma weight residual 114.62 102.54 12.08 1.14e+00 7.69e-01 1.12e+02 angle pdb=" N ARG R 61 " pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 114.75 101.91 12.84 1.26e+00 6.30e-01 1.04e+02 angle pdb=" N ARG P 61 " pdb=" CA ARG P 61 " pdb=" C ARG P 61 " ideal model delta sigma weight residual 114.75 102.08 12.67 1.26e+00 6.30e-01 1.01e+02 ... (remaining 27843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 11356 16.37 - 32.75: 238 32.75 - 49.12: 97 49.12 - 65.50: 70 65.50 - 81.87: 11 Dihedral angle restraints: 11772 sinusoidal: 4375 harmonic: 7397 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual 93.00 39.30 53.70 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CD ARG D 56 " pdb=" NE ARG D 56 " pdb=" CZ ARG D 56 " pdb=" NH1 ARG D 56 " ideal model delta sinusoidal sigma weight residual 0.00 -53.57 53.57 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 45.63 47.37 1 1.00e+01 1.00e-02 3.10e+01 ... (remaining 11769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1688 0.070 - 0.139: 893 0.139 - 0.209: 309 0.209 - 0.278: 71 0.278 - 0.348: 3 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA THR G 24 " pdb=" N THR G 24 " pdb=" C THR G 24 " pdb=" CB THR G 24 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE T 48 " pdb=" CA ILE T 48 " pdb=" CG1 ILE T 48 " pdb=" CG2 ILE T 48 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA MET H 34 " pdb=" N MET H 34 " pdb=" C MET H 34 " pdb=" CB MET H 34 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2961 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 56 " 0.887 9.50e-02 1.11e+02 3.97e-01 9.57e+01 pdb=" NE ARG D 56 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG D 56 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 56 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 56 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 50 " -0.031 2.00e-02 2.50e+03 6.13e-02 3.76e+01 pdb=" C ILE F 50 " 0.106 2.00e-02 2.50e+03 pdb=" O ILE F 50 " -0.040 2.00e-02 2.50e+03 pdb=" N ILE F 51 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 31 " 0.067 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR L 31 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR L 31 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR L 31 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR L 31 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR L 31 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR L 31 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 31 " 0.059 2.00e-02 2.50e+03 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2510 2.72 - 3.26: 17847 3.26 - 3.81: 34285 3.81 - 4.35: 44633 4.35 - 4.90: 71950 Nonbonded interactions: 171225 Sorted by model distance: nonbonded pdb=" N ASP G 101 " pdb=" OD1 ASP G 101 " model vdw 2.175 2.520 nonbonded pdb=" N PRO E 42 " pdb=" O PRO E 42 " model vdw 2.260 2.496 nonbonded pdb=" O ILE F 51 " pdb=" O TRP F 52 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP J 72 " pdb=" NZ LYS J 75 " model vdw 2.349 2.520 nonbonded pdb=" O ARG D 56 " pdb=" CG ASN D 57 " model vdw 2.356 3.270 ... (remaining 171220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Extract box with map and model: 6.310 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 54.390 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.021 0.178 20437 Z= 1.363 Angle : 1.807 13.785 27848 Z= 1.209 Chirality : 0.091 0.348 2964 Planarity : 0.012 0.397 3633 Dihedral : 9.725 81.871 7104 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.01 % Favored : 95.61 % Rotamer: Outliers : 0.24 % Allowed : 0.47 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.66 (0.15), residues: 1078 loop : 0.17 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.008 TRP T 35 HIS 0.029 0.008 HIS U 34 PHE 0.038 0.007 PHE G 67 TYR 0.067 0.009 TYR L 31 ARG 0.010 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 731 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASN cc_start: 0.8254 (m-40) cc_final: 0.8018 (m110) REVERT: H 48 VAL cc_start: 0.8872 (t) cc_final: 0.8664 (t) REVERT: H 109 VAL cc_start: 0.7008 (t) cc_final: 0.6800 (t) REVERT: L 37 GLN cc_start: 0.7585 (tt0) cc_final: 0.7368 (tm-30) REVERT: L 47 LEU cc_start: 0.8486 (tp) cc_final: 0.8275 (tp) REVERT: L 48 ILE cc_start: 0.8936 (mm) cc_final: 0.8712 (mt) REVERT: L 92 ASP cc_start: 0.7286 (t0) cc_final: 0.7065 (m-30) REVERT: A 3 GLN cc_start: 0.7771 (tt0) cc_final: 0.7443 (mp10) REVERT: A 29 PHE cc_start: 0.8555 (t80) cc_final: 0.7943 (t80) REVERT: A 86 ASP cc_start: 0.8088 (m-30) cc_final: 0.7858 (m-30) REVERT: N 21 ILE cc_start: 0.7735 (mp) cc_final: 0.7214 (mt) REVERT: N 82 ASP cc_start: 0.5906 (m-30) cc_final: 0.5596 (m-30) REVERT: N 92 ASP cc_start: 0.8042 (t0) cc_final: 0.7694 (t0) REVERT: N 95 LEU cc_start: 0.9013 (mt) cc_final: 0.8693 (mp) REVERT: N 104 LEU cc_start: 0.8384 (tp) cc_final: 0.8147 (tp) REVERT: B 34 MET cc_start: 0.9014 (mmm) cc_final: 0.8364 (mmp) REVERT: B 82 LEU cc_start: 0.8878 (mt) cc_final: 0.8240 (tp) REVERT: O 105 THR cc_start: 0.7621 (m) cc_final: 0.7389 (p) REVERT: C 82 LEU cc_start: 0.8904 (mp) cc_final: 0.8650 (tp) REVERT: Q 60 ASP cc_start: 0.8174 (t0) cc_final: 0.7935 (t0) REVERT: Q 105 THR cc_start: 0.7796 (m) cc_final: 0.7431 (p) REVERT: F 82 LEU cc_start: 0.9334 (mt) cc_final: 0.9109 (mt) REVERT: F 101 ASP cc_start: 0.8718 (p0) cc_final: 0.8516 (p0) REVERT: R 105 THR cc_start: 0.8458 (m) cc_final: 0.7879 (p) REVERT: G 64 GLU cc_start: 0.7893 (tt0) cc_final: 0.7608 (tt0) REVERT: S 106 LEU cc_start: 0.8046 (mt) cc_final: 0.7769 (tt) REVERT: T 79 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7486 (mt0) REVERT: J 108 LEU cc_start: 0.7905 (tp) cc_final: 0.7614 (tt) REVERT: U 78 LEU cc_start: 0.8865 (tp) cc_final: 0.8589 (tt) REVERT: K 56 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8434 (mmm-85) REVERT: K 100 THR cc_start: 0.8657 (p) cc_final: 0.8405 (p) REVERT: V 5 THR cc_start: 0.7920 (m) cc_final: 0.7696 (p) outliers start: 5 outliers final: 4 residues processed: 735 average time/residue: 0.3808 time to fit residues: 402.6451 Evaluate side-chains 423 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 419 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN O 6 GLN F 73 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN J 105 GLN U 53 ASN M 31 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20437 Z= 0.279 Angle : 0.744 9.160 27848 Z= 0.404 Chirality : 0.047 0.250 2964 Planarity : 0.005 0.062 3633 Dihedral : 5.393 57.718 2941 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.16 % Favored : 95.69 % Rotamer: Outliers : 2.94 % Allowed : 12.01 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.74 (0.15), residues: 1056 loop : -0.06 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 103 HIS 0.005 0.001 HIS H 35 PHE 0.027 0.002 PHE L 62 TYR 0.030 0.002 TYR H 52A ARG 0.010 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 500 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.6592 (ttp80) cc_final: 0.6386 (ttp80) REVERT: H 37 VAL cc_start: 0.8845 (t) cc_final: 0.8549 (p) REVERT: H 80 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7271 (tt) REVERT: H 109 VAL cc_start: 0.7070 (t) cc_final: 0.6706 (t) REVERT: L 54 ARG cc_start: 0.6613 (mtm-85) cc_final: 0.6395 (mtm110) REVERT: L 92 ASP cc_start: 0.7295 (t0) cc_final: 0.6967 (t0) REVERT: A 3 GLN cc_start: 0.7752 (tt0) cc_final: 0.7450 (mp10) REVERT: A 32 TYR cc_start: 0.8579 (m-80) cc_final: 0.8064 (m-10) REVERT: A 72 ASP cc_start: 0.7113 (t0) cc_final: 0.6820 (t0) REVERT: N 21 ILE cc_start: 0.7572 (mp) cc_final: 0.7229 (mt) REVERT: B 75 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8631 (mmtm) REVERT: C 82 LEU cc_start: 0.8915 (mp) cc_final: 0.8523 (mt) REVERT: C 105 GLN cc_start: 0.8107 (pm20) cc_final: 0.7879 (pp30) REVERT: Q 4 LEU cc_start: 0.9100 (mt) cc_final: 0.8820 (mp) REVERT: Q 60 ASP cc_start: 0.7688 (t0) cc_final: 0.7395 (t0) REVERT: R 69 THR cc_start: 0.8722 (p) cc_final: 0.8304 (t) REVERT: S 106 LEU cc_start: 0.8148 (mt) cc_final: 0.7765 (tt) REVERT: T 69 THR cc_start: 0.8084 (p) cc_final: 0.7793 (t) REVERT: J 53 ASP cc_start: 0.8216 (p0) cc_final: 0.7978 (p0) REVERT: J 105 GLN cc_start: 0.8376 (mm110) cc_final: 0.8085 (pm20) REVERT: J 111 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8552 (m) REVERT: U 69 THR cc_start: 0.8707 (p) cc_final: 0.8220 (t) REVERT: K 53 ASP cc_start: 0.8667 (p0) cc_final: 0.8218 (p0) REVERT: K 56 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.8324 (mmm-85) REVERT: V 5 THR cc_start: 0.7865 (m) cc_final: 0.7532 (p) REVERT: V 104 LEU cc_start: 0.9045 (tt) cc_final: 0.8837 (tp) REVERT: M 29 PHE cc_start: 0.8202 (t80) cc_final: 0.7882 (t80) REVERT: W 34 HIS cc_start: 0.7595 (m90) cc_final: 0.6744 (m-70) outliers start: 62 outliers final: 35 residues processed: 527 average time/residue: 0.3333 time to fit residues: 264.0076 Evaluate side-chains 453 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 416 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 212 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN N 37 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN O 34 HIS P 34 HIS P 79 GLN Q 34 HIS R 34 HIS G 57 ASN U 34 HIS ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 20437 Z= 0.438 Angle : 0.727 8.876 27848 Z= 0.391 Chirality : 0.046 0.170 2964 Planarity : 0.005 0.053 3633 Dihedral : 5.201 54.733 2931 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 4.37 % Allowed : 12.16 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.77 (0.15), residues: 1045 loop : -0.35 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.007 0.001 HIS L 34 PHE 0.022 0.003 PHE O 98 TYR 0.023 0.002 TYR H 52A ARG 0.005 0.001 ARG I 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 428 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.5652 (t80) cc_final: 0.5426 (t80) REVERT: H 37 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8562 (p) REVERT: H 39 GLN cc_start: 0.5526 (tt0) cc_final: 0.5312 (tt0) REVERT: H 78 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.6922 (tp) REVERT: H 100 TYR cc_start: 0.7528 (p90) cc_final: 0.7081 (p90) REVERT: L 36 TYR cc_start: 0.6434 (m-80) cc_final: 0.5628 (m-80) REVERT: L 92 ASP cc_start: 0.7174 (t0) cc_final: 0.6939 (t0) REVERT: A 3 GLN cc_start: 0.8065 (tt0) cc_final: 0.7753 (pp30) REVERT: A 29 PHE cc_start: 0.8618 (t80) cc_final: 0.8287 (t80) REVERT: A 32 TYR cc_start: 0.8670 (m-80) cc_final: 0.7971 (m-10) REVERT: A 46 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 72 ASP cc_start: 0.7017 (t0) cc_final: 0.6808 (t0) REVERT: N 21 ILE cc_start: 0.7944 (mp) cc_final: 0.7672 (mt) REVERT: B 75 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8715 (mmtm) REVERT: O 83 GLU cc_start: 0.8135 (tp30) cc_final: 0.7409 (pm20) REVERT: Q 60 ASP cc_start: 0.7766 (t0) cc_final: 0.7501 (t0) REVERT: S 78 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8916 (mt) REVERT: S 106 LEU cc_start: 0.8202 (mt) cc_final: 0.7817 (tt) REVERT: T 69 THR cc_start: 0.8203 (p) cc_final: 0.7932 (t) REVERT: J 16 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7338 (mmt180) REVERT: J 101 ASP cc_start: 0.8686 (p0) cc_final: 0.8464 (p0) REVERT: U 69 THR cc_start: 0.8729 (p) cc_final: 0.8231 (t) REVERT: U 81 GLU cc_start: 0.8137 (mp0) cc_final: 0.7347 (mp0) REVERT: K 4 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8104 (mp) REVERT: K 53 ASP cc_start: 0.8731 (p0) cc_final: 0.8290 (p0) REVERT: K 56 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.8518 (mmm-85) REVERT: K 78 LEU cc_start: 0.9078 (tp) cc_final: 0.8795 (tp) REVERT: V 5 THR cc_start: 0.7855 (m) cc_final: 0.7503 (p) REVERT: M 29 PHE cc_start: 0.8201 (t80) cc_final: 0.7865 (t80) REVERT: W 34 HIS cc_start: 0.7472 (m90) cc_final: 0.6610 (m-70) REVERT: W 49 TYR cc_start: 0.8188 (p90) cc_final: 0.7950 (p90) outliers start: 92 outliers final: 54 residues processed: 468 average time/residue: 0.3356 time to fit residues: 236.7540 Evaluate side-chains 437 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 379 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 52 ILE Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 52 ILE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN N 79 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AASN J 105 GLN ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20437 Z= 0.214 Angle : 0.627 8.829 27848 Z= 0.329 Chirality : 0.043 0.168 2964 Planarity : 0.004 0.063 3633 Dihedral : 4.951 58.108 2931 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 3.47 % Allowed : 14.43 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.95 (0.15), residues: 935 loop : -0.33 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 36 HIS 0.006 0.001 HIS H 35 PHE 0.015 0.002 PHE V 62 TYR 0.020 0.001 TYR H 52A ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 431 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8087 (mt) cc_final: 0.7848 (mt) REVERT: H 34 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8308 (tmm) REVERT: H 37 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8656 (p) REVERT: H 39 GLN cc_start: 0.5483 (tt0) cc_final: 0.5264 (tt0) REVERT: H 56 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7354 (mmt180) REVERT: H 67 PHE cc_start: 0.7795 (m-10) cc_final: 0.7581 (m-10) REVERT: H 97 TYR cc_start: 0.7215 (t80) cc_final: 0.6820 (t80) REVERT: H 100 TYR cc_start: 0.7409 (p90) cc_final: 0.6990 (p90) REVERT: L 36 TYR cc_start: 0.6512 (m-80) cc_final: 0.5748 (m-80) REVERT: L 92 ASP cc_start: 0.7208 (t0) cc_final: 0.6898 (t0) REVERT: A 3 GLN cc_start: 0.8119 (tt0) cc_final: 0.7810 (pp30) REVERT: A 29 PHE cc_start: 0.8442 (t80) cc_final: 0.8028 (t80) REVERT: A 32 TYR cc_start: 0.8712 (m-80) cc_final: 0.8299 (m-10) REVERT: A 72 ASP cc_start: 0.6912 (t0) cc_final: 0.6683 (t0) REVERT: N 21 ILE cc_start: 0.8092 (mp) cc_final: 0.7850 (mt) REVERT: N 106 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7192 (tt) REVERT: B 75 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8861 (mmtm) REVERT: C 3 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8084 (mm-40) REVERT: Q 60 ASP cc_start: 0.7752 (t0) cc_final: 0.7308 (t0) REVERT: F 56 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8833 (mtp-110) REVERT: R 69 THR cc_start: 0.8915 (p) cc_final: 0.8615 (t) REVERT: R 79 GLN cc_start: 0.8356 (mp10) cc_final: 0.7821 (mp10) REVERT: S 106 LEU cc_start: 0.8296 (mt) cc_final: 0.7816 (tt) REVERT: I 4 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (mt) REVERT: T 69 THR cc_start: 0.8084 (p) cc_final: 0.7835 (t) REVERT: U 69 THR cc_start: 0.8658 (p) cc_final: 0.8222 (t) REVERT: U 79 GLN cc_start: 0.8120 (tt0) cc_final: 0.7516 (tt0) REVERT: K 4 LEU cc_start: 0.8371 (mp) cc_final: 0.7687 (mt) REVERT: K 53 ASP cc_start: 0.8677 (p0) cc_final: 0.8213 (p0) REVERT: K 56 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.8388 (mmm-85) REVERT: K 78 LEU cc_start: 0.9025 (tp) cc_final: 0.8783 (tp) REVERT: K 98 TYR cc_start: 0.8269 (t80) cc_final: 0.8051 (t80) REVERT: V 5 THR cc_start: 0.7869 (m) cc_final: 0.7510 (p) REVERT: V 103 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8584 (tptt) REVERT: M 29 PHE cc_start: 0.8157 (t80) cc_final: 0.7839 (t80) REVERT: W 34 HIS cc_start: 0.7519 (m-70) cc_final: 0.6657 (m-70) REVERT: W 49 TYR cc_start: 0.8196 (p90) cc_final: 0.7923 (p90) outliers start: 73 outliers final: 42 residues processed: 464 average time/residue: 0.3256 time to fit residues: 228.8114 Evaluate side-chains 438 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 391 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 129 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN C 81 GLN P 79 GLN ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20437 Z= 0.330 Angle : 0.640 8.445 27848 Z= 0.337 Chirality : 0.044 0.208 2964 Planarity : 0.004 0.063 3633 Dihedral : 4.908 59.386 2931 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 3.80 % Allowed : 15.15 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.00 (0.15), residues: 935 loop : -0.46 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.002 PHE G 67 TYR 0.031 0.002 TYR V 91 ARG 0.014 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 406 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8098 (mt) cc_final: 0.7822 (mt) REVERT: H 34 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: H 37 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (p) REVERT: H 39 GLN cc_start: 0.5623 (tt0) cc_final: 0.5395 (tt0) REVERT: H 47 TRP cc_start: 0.7704 (t60) cc_final: 0.6893 (t60) REVERT: H 56 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7622 (mmt180) REVERT: H 67 PHE cc_start: 0.7770 (m-10) cc_final: 0.7527 (m-10) REVERT: H 97 TYR cc_start: 0.7351 (t80) cc_final: 0.6998 (t80) REVERT: H 100 TYR cc_start: 0.7426 (p90) cc_final: 0.6968 (p90) REVERT: L 36 TYR cc_start: 0.6384 (m-80) cc_final: 0.5741 (m-80) REVERT: L 37 GLN cc_start: 0.7884 (tt0) cc_final: 0.7557 (tp-100) REVERT: L 92 ASP cc_start: 0.7330 (t0) cc_final: 0.7107 (t0) REVERT: L 95 LEU cc_start: 0.8477 (tp) cc_final: 0.8220 (tp) REVERT: A 3 GLN cc_start: 0.8228 (tt0) cc_final: 0.7971 (pp30) REVERT: A 32 TYR cc_start: 0.8731 (m-80) cc_final: 0.8340 (m-10) REVERT: A 72 ASP cc_start: 0.7010 (t0) cc_final: 0.6779 (t0) REVERT: N 21 ILE cc_start: 0.8200 (mp) cc_final: 0.7997 (mt) REVERT: B 75 LYS cc_start: 0.9076 (mmtm) cc_final: 0.8859 (mmtm) REVERT: Q 60 ASP cc_start: 0.7754 (t0) cc_final: 0.7442 (t0) REVERT: F 43 LYS cc_start: 0.9267 (mmtm) cc_final: 0.9058 (mmtm) REVERT: F 56 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8901 (mtp-110) REVERT: R 79 GLN cc_start: 0.8421 (mp10) cc_final: 0.7919 (mp10) REVERT: S 79 GLN cc_start: 0.7362 (mt0) cc_final: 0.7002 (mt0) REVERT: S 106 LEU cc_start: 0.8286 (mt) cc_final: 0.7811 (tt) REVERT: I 4 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8586 (mt) REVERT: T 69 THR cc_start: 0.8226 (p) cc_final: 0.8012 (t) REVERT: U 69 THR cc_start: 0.8679 (p) cc_final: 0.8237 (t) REVERT: U 79 GLN cc_start: 0.8141 (tt0) cc_final: 0.7665 (tt0) REVERT: K 4 LEU cc_start: 0.8382 (mp) cc_final: 0.7656 (mt) REVERT: K 53 ASP cc_start: 0.8700 (p0) cc_final: 0.8258 (p0) REVERT: K 78 LEU cc_start: 0.9104 (tp) cc_final: 0.8895 (tp) REVERT: V 5 THR cc_start: 0.7923 (m) cc_final: 0.7632 (p) REVERT: V 61 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8328 (mtm-85) REVERT: V 103 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8734 (tptt) REVERT: M 29 PHE cc_start: 0.8224 (t80) cc_final: 0.7892 (t80) REVERT: M 100 TYR cc_start: 0.7320 (p90) cc_final: 0.7111 (p90) REVERT: W 34 HIS cc_start: 0.7457 (m-70) cc_final: 0.6276 (m-70) REVERT: W 49 TYR cc_start: 0.8196 (p90) cc_final: 0.7768 (p90) outliers start: 80 outliers final: 63 residues processed: 445 average time/residue: 0.3137 time to fit residues: 212.8613 Evaluate side-chains 452 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 385 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 52 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.8980 chunk 228 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 148 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 253 optimal weight: 50.0000 chunk 210 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 chunk 21 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 79 GLN P 79 GLN ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN W 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20437 Z= 0.157 Angle : 0.592 9.751 27848 Z= 0.305 Chirality : 0.042 0.160 2964 Planarity : 0.004 0.060 3633 Dihedral : 4.679 57.640 2931 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.84 % Rotamer: Outliers : 3.23 % Allowed : 15.72 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.15 (0.15), residues: 935 loop : -0.42 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP W 35 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE V 62 TYR 0.036 0.001 TYR V 91 ARG 0.007 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 422 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.9006 (t) cc_final: 0.8649 (p) REVERT: H 39 GLN cc_start: 0.5452 (tt0) cc_final: 0.5241 (tt0) REVERT: H 56 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7612 (mmt180) REVERT: H 67 PHE cc_start: 0.7731 (m-10) cc_final: 0.7459 (m-10) REVERT: H 82 MET cc_start: 0.7386 (mtp) cc_final: 0.7093 (mtp) REVERT: H 97 TYR cc_start: 0.7225 (t80) cc_final: 0.6763 (t80) REVERT: H 100 TYR cc_start: 0.7375 (p90) cc_final: 0.6758 (p90) REVERT: L 36 TYR cc_start: 0.6435 (m-80) cc_final: 0.5801 (m-80) REVERT: L 92 ASP cc_start: 0.7148 (t0) cc_final: 0.6803 (t0) REVERT: A 3 GLN cc_start: 0.8254 (tt0) cc_final: 0.7991 (pp30) REVERT: A 29 PHE cc_start: 0.8411 (t80) cc_final: 0.8010 (t80) REVERT: A 32 TYR cc_start: 0.8645 (m-80) cc_final: 0.8305 (m-10) REVERT: N 21 ILE cc_start: 0.8199 (mp) cc_final: 0.7999 (mt) REVERT: B 72 ASP cc_start: 0.7855 (t0) cc_final: 0.7037 (t0) REVERT: B 75 LYS cc_start: 0.9037 (mmtm) cc_final: 0.8505 (mmtm) REVERT: C 43 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8239 (mmtp) REVERT: C 57 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: Q 60 ASP cc_start: 0.7705 (t0) cc_final: 0.7418 (t0) REVERT: Q 69 THR cc_start: 0.8719 (p) cc_final: 0.8476 (t) REVERT: R 69 THR cc_start: 0.8924 (p) cc_final: 0.8699 (t) REVERT: R 79 GLN cc_start: 0.8397 (mp10) cc_final: 0.8081 (mp10) REVERT: S 79 GLN cc_start: 0.7146 (mt0) cc_final: 0.6901 (mt0) REVERT: S 106 LEU cc_start: 0.8282 (mt) cc_final: 0.7930 (tt) REVERT: I 4 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8460 (mt) REVERT: I 34 MET cc_start: 0.8773 (mmt) cc_final: 0.8516 (mmt) REVERT: T 69 THR cc_start: 0.8114 (p) cc_final: 0.7912 (t) REVERT: U 69 THR cc_start: 0.8643 (p) cc_final: 0.8208 (t) REVERT: U 79 GLN cc_start: 0.8192 (tt0) cc_final: 0.7663 (tt0) REVERT: K 28 THR cc_start: 0.9526 (m) cc_final: 0.9177 (p) REVERT: K 53 ASP cc_start: 0.8733 (p0) cc_final: 0.8307 (p0) REVERT: V 61 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8297 (mtm-85) REVERT: V 103 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8595 (tptt) REVERT: V 104 LEU cc_start: 0.9047 (tt) cc_final: 0.8669 (tp) REVERT: M 29 PHE cc_start: 0.8175 (t80) cc_final: 0.7907 (t80) REVERT: W 34 HIS cc_start: 0.7030 (m-70) cc_final: 0.6161 (m-70) outliers start: 68 outliers final: 47 residues processed: 455 average time/residue: 0.3224 time to fit residues: 223.8168 Evaluate side-chains 451 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 402 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN O 37 GLN P 79 GLN G 57 ASN ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20437 Z= 0.461 Angle : 0.692 8.616 27848 Z= 0.362 Chirality : 0.045 0.176 2964 Planarity : 0.005 0.063 3633 Dihedral : 4.815 21.563 2927 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 3.47 % Allowed : 16.19 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.98 (0.16), residues: 935 loop : -0.60 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP W 35 HIS 0.007 0.001 HIS H 35 PHE 0.025 0.002 PHE G 67 TYR 0.025 0.002 TYR W 91 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 386 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.5821 (t80) cc_final: 0.5583 (t80) REVERT: H 37 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (p) REVERT: H 39 GLN cc_start: 0.5736 (tt0) cc_final: 0.5468 (tt0) REVERT: H 67 PHE cc_start: 0.7644 (m-10) cc_final: 0.7383 (m-10) REVERT: H 97 TYR cc_start: 0.7312 (t80) cc_final: 0.7069 (t80) REVERT: H 100 TYR cc_start: 0.7464 (p90) cc_final: 0.6894 (p90) REVERT: L 36 TYR cc_start: 0.6247 (m-80) cc_final: 0.5661 (m-80) REVERT: L 37 GLN cc_start: 0.7829 (tt0) cc_final: 0.7368 (tp-100) REVERT: A 32 TYR cc_start: 0.8755 (m-80) cc_final: 0.8412 (m-10) REVERT: B 72 ASP cc_start: 0.8003 (t0) cc_final: 0.7256 (t0) REVERT: B 75 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8534 (mmtm) REVERT: Q 60 ASP cc_start: 0.7831 (t0) cc_final: 0.7558 (t0) REVERT: R 78 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9005 (tt) REVERT: R 79 GLN cc_start: 0.8490 (mp10) cc_final: 0.7875 (mp10) REVERT: S 79 GLN cc_start: 0.7252 (mt0) cc_final: 0.6790 (mt0) REVERT: I 4 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8510 (mt) REVERT: I 72 ASP cc_start: 0.8354 (t0) cc_final: 0.8148 (t0) REVERT: T 69 THR cc_start: 0.8362 (p) cc_final: 0.8138 (t) REVERT: J 16 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7651 (mmt180) REVERT: U 69 THR cc_start: 0.8681 (p) cc_final: 0.8211 (t) REVERT: U 79 GLN cc_start: 0.8063 (tt0) cc_final: 0.7592 (tt0) REVERT: U 81 GLU cc_start: 0.8322 (mp0) cc_final: 0.7727 (pm20) REVERT: K 53 ASP cc_start: 0.8746 (p0) cc_final: 0.8275 (p0) REVERT: V 61 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: V 79 GLN cc_start: 0.8268 (mm110) cc_final: 0.7977 (mm110) REVERT: V 103 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8731 (tptt) REVERT: M 29 PHE cc_start: 0.8236 (t80) cc_final: 0.7984 (t80) REVERT: M 97 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.3565 (p90) outliers start: 73 outliers final: 59 residues processed: 419 average time/residue: 0.3291 time to fit residues: 207.2119 Evaluate side-chains 435 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 372 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 97 TYR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 0.0060 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20437 Z= 0.193 Angle : 0.623 9.418 27848 Z= 0.318 Chirality : 0.042 0.166 2964 Planarity : 0.004 0.061 3633 Dihedral : 4.599 22.286 2927 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.89 % Favored : 93.99 % Rotamer: Outliers : 3.13 % Allowed : 17.00 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.12 (0.16), residues: 935 loop : -0.55 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP W 35 HIS 0.008 0.001 HIS H 35 PHE 0.013 0.001 PHE V 62 TYR 0.026 0.001 TYR W 91 ARG 0.007 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 414 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8640 (p) REVERT: H 39 GLN cc_start: 0.5543 (tt0) cc_final: 0.5269 (tt0) REVERT: H 56 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7332 (mmt180) REVERT: H 97 TYR cc_start: 0.7334 (t80) cc_final: 0.7075 (t80) REVERT: H 100 TYR cc_start: 0.7371 (p90) cc_final: 0.6849 (p90) REVERT: L 36 TYR cc_start: 0.6609 (m-80) cc_final: 0.5968 (m-80) REVERT: L 92 ASP cc_start: 0.6304 (t0) cc_final: 0.5951 (t0) REVERT: A 32 TYR cc_start: 0.8670 (m-80) cc_final: 0.8392 (m-10) REVERT: A 83 ARG cc_start: 0.8048 (mpp80) cc_final: 0.7707 (mpp80) REVERT: B 72 ASP cc_start: 0.7868 (t0) cc_final: 0.6979 (t0) REVERT: B 75 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8541 (mmtm) REVERT: O 60 ASP cc_start: 0.7786 (t70) cc_final: 0.7550 (t0) REVERT: C 43 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8187 (mmtp) REVERT: Q 60 ASP cc_start: 0.7694 (t0) cc_final: 0.7418 (t0) REVERT: R 69 THR cc_start: 0.8975 (p) cc_final: 0.8757 (t) REVERT: R 78 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8981 (tt) REVERT: R 79 GLN cc_start: 0.8409 (mp10) cc_final: 0.7801 (mp10) REVERT: S 79 GLN cc_start: 0.7018 (mt0) cc_final: 0.6772 (mt0) REVERT: I 4 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8471 (mt) REVERT: T 69 THR cc_start: 0.8272 (p) cc_final: 0.8059 (t) REVERT: J 16 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7643 (mmt180) REVERT: U 69 THR cc_start: 0.8670 (p) cc_final: 0.8237 (t) REVERT: U 79 GLN cc_start: 0.8018 (tt0) cc_final: 0.7480 (tt0) REVERT: U 106 LEU cc_start: 0.8168 (mp) cc_final: 0.7584 (pp) REVERT: K 53 ASP cc_start: 0.8771 (p0) cc_final: 0.8310 (p0) REVERT: V 61 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8254 (mtm-85) REVERT: V 79 GLN cc_start: 0.8306 (mm110) cc_final: 0.7990 (mm110) REVERT: V 103 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8684 (tptt) REVERT: M 29 PHE cc_start: 0.8199 (t80) cc_final: 0.7926 (t80) outliers start: 66 outliers final: 55 residues processed: 445 average time/residue: 0.3290 time to fit residues: 221.1427 Evaluate side-chains 455 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 397 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 141 optimal weight: 0.0570 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 72 optimal weight: 0.0060 chunk 212 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 overall best weight: 1.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20437 Z= 0.203 Angle : 0.627 9.675 27848 Z= 0.319 Chirality : 0.043 0.180 2964 Planarity : 0.004 0.060 3633 Dihedral : 4.495 20.635 2927 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 2.99 % Allowed : 17.62 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.13 (0.15), residues: 957 loop : -0.53 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP W 35 HIS 0.009 0.001 HIS H 35 PHE 0.016 0.002 PHE K 67 TYR 0.031 0.001 TYR W 91 ARG 0.007 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 399 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8649 (p) REVERT: H 39 GLN cc_start: 0.5521 (tt0) cc_final: 0.5248 (tt0) REVERT: H 56 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7204 (mmt180) REVERT: H 97 TYR cc_start: 0.7338 (t80) cc_final: 0.7031 (t80) REVERT: H 100 TYR cc_start: 0.7408 (p90) cc_final: 0.6885 (p90) REVERT: L 36 TYR cc_start: 0.6591 (m-80) cc_final: 0.5998 (m-80) REVERT: L 92 ASP cc_start: 0.6301 (t0) cc_final: 0.6044 (t0) REVERT: A 32 TYR cc_start: 0.8673 (m-80) cc_final: 0.8380 (m-10) REVERT: B 72 ASP cc_start: 0.7905 (t0) cc_final: 0.7031 (t0) REVERT: B 75 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8544 (mmtm) REVERT: O 60 ASP cc_start: 0.7869 (t70) cc_final: 0.7634 (t0) REVERT: C 43 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8304 (mmtp) REVERT: Q 60 ASP cc_start: 0.7659 (t0) cc_final: 0.7441 (t0) REVERT: R 69 THR cc_start: 0.8965 (p) cc_final: 0.8761 (t) REVERT: R 79 GLN cc_start: 0.8404 (mp10) cc_final: 0.7739 (mp10) REVERT: S 79 GLN cc_start: 0.7074 (mt0) cc_final: 0.6785 (mt0) REVERT: I 4 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8495 (mt) REVERT: T 69 THR cc_start: 0.8285 (p) cc_final: 0.8073 (t) REVERT: U 69 THR cc_start: 0.8676 (p) cc_final: 0.8252 (t) REVERT: U 79 GLN cc_start: 0.8046 (tt0) cc_final: 0.7341 (tt0) REVERT: U 81 GLU cc_start: 0.8232 (mp0) cc_final: 0.7523 (pm20) REVERT: U 106 LEU cc_start: 0.8273 (mp) cc_final: 0.7661 (pp) REVERT: K 53 ASP cc_start: 0.8767 (p0) cc_final: 0.8301 (p0) REVERT: K 79 TYR cc_start: 0.8752 (m-80) cc_final: 0.8544 (m-80) REVERT: V 61 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8256 (mtm-85) REVERT: V 103 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8679 (tptt) REVERT: V 104 LEU cc_start: 0.9129 (tt) cc_final: 0.8717 (tp) REVERT: M 29 PHE cc_start: 0.8136 (t80) cc_final: 0.7910 (t80) REVERT: M 98 TYR cc_start: 0.6985 (t80) cc_final: 0.6474 (t80) outliers start: 63 outliers final: 57 residues processed: 431 average time/residue: 0.3211 time to fit residues: 209.2331 Evaluate side-chains 450 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 391 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 151 optimal weight: 0.0070 chunk 118 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 240 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20437 Z= 0.177 Angle : 0.628 10.696 27848 Z= 0.317 Chirality : 0.043 0.170 2964 Planarity : 0.004 0.072 3633 Dihedral : 4.371 21.231 2927 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 2.56 % Allowed : 18.47 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.16 (0.15), residues: 957 loop : -0.51 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP W 35 HIS 0.009 0.001 HIS H 35 PHE 0.020 0.001 PHE H 29 TYR 0.031 0.001 TYR V 91 ARG 0.017 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 403 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8665 (p) REVERT: H 39 GLN cc_start: 0.5499 (tt0) cc_final: 0.5231 (tt0) REVERT: H 47 TRP cc_start: 0.7675 (t60) cc_final: 0.6926 (t60) REVERT: H 56 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7296 (mmt180) REVERT: H 97 TYR cc_start: 0.7253 (t80) cc_final: 0.6966 (t80) REVERT: H 100 TYR cc_start: 0.7375 (p90) cc_final: 0.6874 (p90) REVERT: L 36 TYR cc_start: 0.6442 (m-80) cc_final: 0.5892 (m-80) REVERT: A 32 TYR cc_start: 0.8612 (m-80) cc_final: 0.8351 (m-10) REVERT: B 72 ASP cc_start: 0.7869 (t0) cc_final: 0.7002 (t0) REVERT: B 75 LYS cc_start: 0.9068 (mmtm) cc_final: 0.8625 (mmtm) REVERT: O 60 ASP cc_start: 0.7791 (t70) cc_final: 0.7575 (t0) REVERT: C 43 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8356 (mmtp) REVERT: F 85 GLU cc_start: 0.8495 (pm20) cc_final: 0.8287 (pm20) REVERT: R 69 THR cc_start: 0.8940 (p) cc_final: 0.8733 (t) REVERT: R 78 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9024 (tt) REVERT: R 79 GLN cc_start: 0.8392 (mp10) cc_final: 0.7771 (mp10) REVERT: I 4 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (mt) REVERT: J 16 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7521 (mmt180) REVERT: U 69 THR cc_start: 0.8689 (p) cc_final: 0.8277 (t) REVERT: U 79 GLN cc_start: 0.8059 (tt0) cc_final: 0.7377 (tt0) REVERT: U 81 GLU cc_start: 0.8259 (mp0) cc_final: 0.7519 (pm20) REVERT: U 106 LEU cc_start: 0.8235 (mp) cc_final: 0.7697 (pp) REVERT: K 28 THR cc_start: 0.9513 (m) cc_final: 0.9186 (p) REVERT: K 53 ASP cc_start: 0.8747 (p0) cc_final: 0.8303 (p0) REVERT: V 61 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: V 103 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8677 (tptt) REVERT: V 104 LEU cc_start: 0.9107 (tt) cc_final: 0.8694 (tp) REVERT: M 98 TYR cc_start: 0.6898 (t80) cc_final: 0.6465 (t80) outliers start: 54 outliers final: 45 residues processed: 431 average time/residue: 0.3203 time to fit residues: 210.5280 Evaluate side-chains 435 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 387 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.8980 chunk 221 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 191 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 57 ASN ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.065214 restraints weight = 48550.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067762 restraints weight = 23080.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069324 restraints weight = 15056.675| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20437 Z= 0.196 Angle : 0.625 9.965 27848 Z= 0.316 Chirality : 0.043 0.202 2964 Planarity : 0.004 0.072 3633 Dihedral : 4.325 18.952 2927 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 2.90 % Allowed : 18.19 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.18 (0.15), residues: 957 loop : -0.50 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP W 35 HIS 0.012 0.001 HIS H 35 PHE 0.022 0.002 PHE M 29 TYR 0.028 0.001 TYR W 91 ARG 0.008 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4676.67 seconds wall clock time: 85 minutes 47.65 seconds (5147.65 seconds total)