Starting phenix.real_space_refine on Fri Sep 27 14:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/09_2024/8dyy_27786.cif" } resolution = 3.62 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= 0.005 sd= 0.065 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 63 5.16 5 C 10379 2.51 5 N 2833 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16499 Number of models: 1 Model: "" Number of chains: 19 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 506 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 18, 'TRANS': 53} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "P" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "Q" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "S" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "T" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "U" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "V" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 10.44, per 1000 atoms: 0.63 Number of scatterers: 16499 At special positions: 0 Unit cell: (110.4, 115, 156.4, 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 63 16.00 O 3224 8.00 N 2833 7.00 C 10379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.2 seconds 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 56 sheets defined 4.5% alpha, 48.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.655A pdb=" N ASN H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.735A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.705A pdb=" N ASN A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.039A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.701A pdb=" N THR E 87 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.915A pdb=" N ASN M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.655A pdb=" N THR M 87 " --> pdb=" O VAL M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.552A pdb=" N ASN O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.971A pdb=" N THR Q 87 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.236A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.735A pdb=" N THR S 87 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR U 87 " --> pdb=" O VAL U 84 " (cutoff:3.500A) 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: 6.091A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.597A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.535A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.427A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 58 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.427A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.618A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.723A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.583A pdb=" N VAL C 89 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.509A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.700A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 67 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.468A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.504A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.541A pdb=" N LEU E 20 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.250A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.250A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.047A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 67 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.522A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.522A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.619A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR M 58 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.795A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.607A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET O 34 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR O 58 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.827A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.577A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR P 49 " --> pdb=" O SER P 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.532A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.810A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.524A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET Q 34 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.524A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 4 through 7 removed outlier: 4.165A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER R 67 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.692A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 85 " --> pdb=" O GLN R 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.692A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.511A pdb=" N CYS S 22 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.210A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET S 34 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.210A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG S 94 " --> pdb=" O ASP S 101 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 4 through 7 removed outlier: 4.259A pdb=" N GLU T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER T 67 " --> pdb=" O GLU T 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.489A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.633A pdb=" N LEU U 20 " --> pdb=" O LEU U 80 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU U 80 " --> pdb=" O LEU U 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.798A pdb=" N MET U 34 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR U 58 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.978A pdb=" N LEU U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.929A pdb=" N GLU V 70 " --> pdb=" O SER V 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER V 67 " --> pdb=" O GLU V 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.535A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.535A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1581 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: 5.40 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.31: 2630 1.31 - 1.60: 14191 1.60 - 1.89: 90 1.89 - 2.18: 0 2.18 - 2.47: 1 Bond restraints: 16912 Sorted by residual: bond pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " ideal model delta sigma weight residual 1.492 2.467 -0.975 5.00e-02 4.00e+02 3.80e+02 bond pdb=" CG PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 1.503 1.024 0.479 3.40e-02 8.65e+02 1.98e+02 bond pdb=" N PRO I 3 " pdb=" CA PRO I 3 " ideal model delta sigma weight residual 1.472 1.398 0.073 1.34e-02 5.57e+03 2.99e+01 bond pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.52e-02 4.33e+03 1.38e+01 ... (remaining 16907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 22984 21.21 - 42.42: 1 42.42 - 63.63: 0 63.63 - 84.85: 0 84.85 - 106.06: 1 Bond angle restraints: 22986 Sorted by residual: angle pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO I 3 " pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 112.00 92.60 19.40 1.40e+00 5.10e-01 1.92e+02 angle pdb=" N PRO I 3 " pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " ideal model delta sigma weight residual 103.26 87.76 15.50 1.14e+00 7.69e-01 1.85e+02 angle pdb=" CA PRO I 3 " pdb=" CB PRO I 3 " pdb=" CG PRO I 3 " ideal model delta sigma weight residual 104.50 93.75 10.75 1.90e+00 2.77e-01 3.20e+01 angle pdb=" C ASP I 2 " pdb=" N PRO I 3 " pdb=" CD PRO I 3 " ideal model delta sigma weight residual 125.00 147.48 -22.48 4.10e+00 5.95e-02 3.01e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 9206 23.61 - 47.21: 545 47.21 - 70.82: 64 70.82 - 94.42: 21 94.42 - 118.03: 1 Dihedral angle restraints: 9837 sinusoidal: 3736 harmonic: 6101 Sorted by residual: 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 93.00 174.54 -81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS U 22 " pdb=" SG CYS U 22 " pdb=" SG CYS U 92 " pdb=" CB CYS U 92 " ideal model delta sinusoidal sigma weight residual -86.00 -164.76 78.76 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 166.86 -73.86 1 1.00e+01 1.00e-02 6.93e+01 ... (remaining 9834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1952 0.050 - 0.100: 407 0.100 - 0.150: 123 0.150 - 0.200: 2 0.200 - 0.250: 1 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA PRO I 3 " pdb=" N PRO I 3 " pdb=" C PRO I 3 " pdb=" CB PRO I 3 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CB THR E 28 " pdb=" CA THR E 28 " pdb=" OG1 THR E 28 " pdb=" CG2 THR E 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2482 not shown) Planarity restraints: 2933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO I 3 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C PRO I 3 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO I 3 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN I 4 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS V 39 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO V 40 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO V 40 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO V 40 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 40 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 41 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.040 5.00e-02 4.00e+02 ... (remaining 2930 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 243 2.65 - 3.21: 14490 3.21 - 3.77: 24459 3.77 - 4.34: 34295 4.34 - 4.90: 60507 Nonbonded interactions: 133994 Sorted by model distance: nonbonded pdb=" OE1 GLN A 3 " pdb=" N LEU A 4 " model vdw 2.085 3.120 nonbonded pdb=" OD1 ASP V 17 " pdb=" N ARG V 18 " model vdw 2.093 3.120 nonbonded pdb=" O HIS C 100B" pdb=" ND1 HIS C 100B" model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP N 17 " pdb=" N ARG N 18 " model vdw 2.185 3.120 nonbonded pdb=" N GLN A 105 " pdb=" OE1 GLN A 105 " model vdw 2.199 3.120 ... (remaining 133989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.330 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.011 0.975 16912 Z= 0.527 Angle : 0.957 106.058 22986 Z= 0.416 Chirality : 0.045 0.250 2485 Planarity : 0.005 0.077 2933 Dihedral : 14.400 118.025 5913 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.33 % Allowed : 14.48 % Favored : 85.19 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 11.11 % 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: -0.11 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.01 (0.17), residues: 1062 loop : 0.00 (0.21), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 52 HIS 0.004 0.001 HIS E 100B PHE 0.015 0.002 PHE M 29 TYR 0.023 0.002 TYR U 52A ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 1.815 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 204 average time/residue: 0.2748 time to fit residues: 85.1147 Evaluate side-chains 205 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 72 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 24 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS O 31 ASN O 39 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Q 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16912 Z= 0.239 Angle : 0.565 8.981 22986 Z= 0.301 Chirality : 0.043 0.166 2485 Planarity : 0.004 0.058 2933 Dihedral : 4.667 49.265 2337 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.71 % Allowed : 12.43 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.28 (0.18), residues: 945 loop : 0.15 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 52 HIS 0.003 0.001 HIS E 97 PHE 0.013 0.001 PHE M 29 TYR 0.015 0.001 TYR U 52A ARG 0.005 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: I 9 VAL cc_start: 0.8572 (m) cc_final: 0.8188 (t) REVERT: H 28 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 86 ASP cc_start: 0.7589 (m-30) cc_final: 0.7375 (m-30) REVERT: D 102 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.7950 (t) REVERT: E 72 ASP cc_start: 0.8200 (t0) cc_final: 0.7981 (t0) REVERT: F 17 ASP cc_start: 0.7654 (t0) cc_final: 0.7445 (t0) REVERT: P 6 GLN cc_start: 0.8032 (mt0) cc_final: 0.7828 (mt0) REVERT: R 100 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8469 (pt0) REVERT: S 108 LEU cc_start: 0.8341 (mt) cc_final: 0.8127 (mt) REVERT: U 79 TYR cc_start: 0.8247 (m-80) cc_final: 0.7984 (m-80) REVERT: V 74 THR cc_start: 0.8196 (m) cc_final: 0.7850 (p) REVERT: V 82 ASP cc_start: 0.8163 (m-30) cc_final: 0.7794 (m-30) outliers start: 49 outliers final: 34 residues processed: 257 average time/residue: 0.2714 time to fit residues: 106.2166 Evaluate side-chains 240 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN I 20 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS E 97 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16912 Z= 0.433 Angle : 0.630 8.151 22986 Z= 0.335 Chirality : 0.045 0.197 2485 Planarity : 0.005 0.052 2933 Dihedral : 4.923 57.968 2332 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.54 % Allowed : 12.65 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.06 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 1035 loop : -0.24 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 47 HIS 0.008 0.001 HIS E 100B PHE 0.020 0.002 PHE M 29 TYR 0.020 0.002 TYR M 52A ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 1.929 Fit side-chains REVERT: A 4 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6894 (mp) REVERT: A 86 ASP cc_start: 0.7644 (m-30) cc_final: 0.7375 (m-30) REVERT: D 102 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8099 (t) REVERT: E 72 ASP cc_start: 0.8282 (t0) cc_final: 0.7999 (t0) REVERT: E 100 ARG cc_start: 0.7455 (tpp-160) cc_final: 0.7112 (tpp-160) REVERT: F 17 ASP cc_start: 0.7660 (t0) cc_final: 0.7435 (t0) REVERT: N 17 ASP cc_start: 0.8163 (t0) cc_final: 0.7817 (t0) REVERT: P 100 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: Q 52 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8049 (t80) REVERT: R 100 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: S 108 LEU cc_start: 0.8492 (mt) cc_final: 0.8269 (mt) REVERT: V 82 ASP cc_start: 0.8276 (m-30) cc_final: 0.7939 (m-30) outliers start: 64 outliers final: 48 residues processed: 249 average time/residue: 0.2681 time to fit residues: 102.0312 Evaluate side-chains 241 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 188 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16912 Z= 0.148 Angle : 0.518 8.647 22986 Z= 0.274 Chirality : 0.042 0.218 2485 Planarity : 0.004 0.048 2933 Dihedral : 4.448 58.831 2332 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.98 % Allowed : 13.54 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.45 (0.18), residues: 936 loop : 0.06 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.019 0.001 HIS C 97 PHE 0.009 0.001 PHE H 29 TYR 0.019 0.001 TYR U 52A ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8635 (m90) REVERT: A 4 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 86 ASP cc_start: 0.7609 (m-30) cc_final: 0.7369 (m-30) REVERT: D 102 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.7993 (t) REVERT: F 17 ASP cc_start: 0.7570 (t0) cc_final: 0.7332 (t0) REVERT: N 17 ASP cc_start: 0.8156 (t0) cc_final: 0.7771 (t0) REVERT: Q 52 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7638 (t80) REVERT: R 100 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: S 79 TYR cc_start: 0.8751 (m-80) cc_final: 0.8497 (m-80) REVERT: U 79 TYR cc_start: 0.8295 (m-80) cc_final: 0.7939 (m-10) REVERT: V 82 ASP cc_start: 0.8178 (m-30) cc_final: 0.7924 (m-30) outliers start: 54 outliers final: 36 residues processed: 263 average time/residue: 0.2727 time to fit residues: 109.7995 Evaluate side-chains 235 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 2 optimal weight: 0.0060 chunk 147 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN A 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16912 Z= 0.228 Angle : 0.536 8.849 22986 Z= 0.283 Chirality : 0.042 0.237 2485 Planarity : 0.004 0.047 2933 Dihedral : 4.432 56.768 2332 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.65 % Allowed : 13.54 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.19 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.45 (0.17), residues: 1035 loop : -0.11 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 103 HIS 0.003 0.001 HIS E 100B PHE 0.012 0.001 PHE H 29 TYR 0.018 0.001 TYR M 52A ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 205 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: H 97 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8659 (m90) REVERT: A 4 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6971 (mp) REVERT: A 86 ASP cc_start: 0.7615 (m-30) cc_final: 0.7339 (m-30) REVERT: B 90 GLN cc_start: 0.7535 (pp30) cc_final: 0.6926 (pp30) REVERT: D 102 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8169 (t) REVERT: F 17 ASP cc_start: 0.7601 (t0) cc_final: 0.7335 (t0) REVERT: N 17 ASP cc_start: 0.8200 (t0) cc_final: 0.7750 (t0) REVERT: Q 16 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7899 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7841 (t80) REVERT: R 100 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: S 79 TYR cc_start: 0.8762 (m-80) cc_final: 0.8444 (m-80) REVERT: U 79 TYR cc_start: 0.8223 (m-80) cc_final: 0.7903 (m-10) REVERT: V 82 ASP cc_start: 0.8212 (m-30) cc_final: 0.7916 (m-30) outliers start: 66 outliers final: 45 residues processed: 249 average time/residue: 0.2695 time to fit residues: 102.3092 Evaluate side-chains 245 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 40.0000 chunk 198 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 HIS Q 97 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16912 Z= 0.344 Angle : 0.586 8.748 22986 Z= 0.310 Chirality : 0.044 0.250 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.683 56.666 2332 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.87 % Allowed : 13.65 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.35 (0.17), residues: 1035 loop : -0.24 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 52 HIS 0.006 0.001 HIS E 100B PHE 0.016 0.002 PHE M 29 TYR 0.019 0.002 TYR U 52A ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4190 Ramachandran restraints generated. 2095 Oldfield, 0 Emsley, 2095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 200 time to evaluate : 1.675 Fit side-chains REVERT: H 97 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8625 (m90) REVERT: A 4 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6931 (mp) REVERT: A 86 ASP cc_start: 0.7583 (m-30) cc_final: 0.7241 (m-30) REVERT: B 90 GLN cc_start: 0.7552 (pp30) cc_final: 0.6931 (pp30) REVERT: C 3 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7063 (tp40) REVERT: C 83 ARG cc_start: 0.7669 (mpp80) cc_final: 0.7459 (mpp80) REVERT: D 102 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8242 (t) REVERT: E 87 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8708 (p) REVERT: F 17 ASP cc_start: 0.7551 (t0) cc_final: 0.7346 (t0) REVERT: N 17 ASP cc_start: 0.8306 (t0) cc_final: 0.7751 (t0) REVERT: P 3 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7171 (mm-40) REVERT: P 100 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: Q 16 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7944 (mpp-170) REVERT: Q 52 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7845 (t80) REVERT: R 100 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: S 79 TYR cc_start: 0.8794 (m-80) cc_final: 0.8360 (m-10) REVERT: U 79 TYR cc_start: 0.8240 (m-80) cc_final: 0.7879 (m-10) REVERT: V 82 ASP cc_start: 0.8280 (m-30) cc_final: 0.7955 (m-30) outliers start: 70 outliers final: 53 residues processed: 249 average time/residue: 0.2630 time to fit residues: 100.3550 Evaluate side-chains 254 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 194 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 52 TYR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain R residue 4 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 4 MET Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1404 > 50: distance: 48 - 66: 36.622 distance: 54 - 58: 29.654 distance: 58 - 59: 30.070 distance: 60 - 61: 9.418 distance: 62 - 63: 39.466 distance: 63 - 64: 49.312 distance: 63 - 65: 30.887 distance: 66 - 67: 21.949 distance: 67 - 68: 40.298 distance: 67 - 70: 58.081 distance: 68 - 69: 15.232 distance: 68 - 78: 46.008 distance: 70 - 71: 18.934 distance: 71 - 72: 14.812 distance: 71 - 73: 29.680 distance: 72 - 74: 17.852 distance: 73 - 75: 34.685 distance: 74 - 76: 8.317 distance: 75 - 76: 17.985 distance: 76 - 77: 18.434 distance: 78 - 79: 23.622 distance: 79 - 80: 12.967 distance: 80 - 81: 9.209 distance: 80 - 82: 12.223 distance: 82 - 83: 32.710 distance: 83 - 84: 13.271 distance: 83 - 86: 17.189 distance: 84 - 85: 15.814 distance: 84 - 90: 29.359 distance: 86 - 87: 5.382 distance: 88 - 89: 37.203 distance: 90 - 91: 23.083 distance: 90 - 302: 24.212 distance: 91 - 92: 13.271 distance: 91 - 94: 11.105 distance: 92 - 93: 35.210 distance: 92 - 100: 27.384 distance: 93 - 299: 37.108 distance: 94 - 95: 43.130 distance: 95 - 96: 17.688 distance: 95 - 97: 19.830 distance: 96 - 98: 25.694 distance: 97 - 99: 39.475 distance: 98 - 99: 14.878 distance: 100 - 101: 11.327 distance: 101 - 102: 39.955 distance: 101 - 104: 6.205 distance: 102 - 103: 21.181 distance: 102 - 114: 7.507 distance: 103 - 192: 31.322 distance: 104 - 105: 19.911 distance: 105 - 106: 3.797 distance: 105 - 107: 15.349 distance: 106 - 108: 32.973 distance: 107 - 109: 26.061 distance: 107 - 110: 25.275 distance: 108 - 109: 26.487 distance: 109 - 111: 36.681 distance: 110 - 112: 23.041 distance: 111 - 113: 16.477 distance: 112 - 113: 29.353 distance: 114 - 115: 12.108 distance: 114 - 285: 16.300 distance: 115 - 116: 32.437 distance: 115 - 118: 17.170 distance: 116 - 117: 25.360 distance: 116 - 121: 31.620 distance: 117 - 282: 22.753 distance: 118 - 119: 15.942 distance: 118 - 120: 13.913 distance: 121 - 122: 20.478 distance: 121 - 180: 7.575 distance: 122 - 123: 36.524 distance: 122 - 125: 14.461 distance: 123 - 124: 10.374 distance: 123 - 132: 34.277 distance: 124 - 177: 22.347 distance: 125 - 126: 49.473 distance: 126 - 127: 55.338 distance: 127 - 128: 29.438 distance: 129 - 130: 14.666 distance: 129 - 131: 20.888 distance: 132 - 133: 19.434 distance: 132 - 267: 24.665 distance: 133 - 134: 19.973 distance: 133 - 136: 13.383 distance: 134 - 135: 25.425 distance: 134 - 141: 20.626 distance: 135 - 264: 20.301 distance: 136 - 137: 31.876 distance: 137 - 138: 18.186 distance: 138 - 139: 27.892 distance: 138 - 140: 6.786 distance: 141 - 142: 21.556 distance: 142 - 143: 19.460 distance: 142 - 145: 8.272 distance: 143 - 144: 6.062 distance: 143 - 148: 24.357 distance: 145 - 146: 3.175 distance: 145 - 147: 14.640