Starting phenix.real_space_refine on Thu Nov 16 20:21:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/11_2023/8dyy_27786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/11_2023/8dyy_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_27786/11_2023/8dyy_27786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/11_2023/8dyy_27786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/11_2023/8dyy_27786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyy_27786/11_2023/8dyy_27786.pdb" } 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 Residue "I ASP 2": "OD1" <-> "OD2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M ASP 85": "OD1" <-> "OD2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 81": "OD1" <-> "OD2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P GLU 105": "OE1" <-> "OE2" Residue "Q ASP 85": "OD1" <-> "OD2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 85": "OD1" <-> "OD2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 72": "OD1" <-> "OD2" Residue "V GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 8.77, per 1000 atoms: 0.53 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 - 3.50 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: 6.60 Conformation dependent library (CDL) restraints added in 3.3 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: 2.49 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: 5.30 Time building geometry restraints manager: 7.13 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: 0.04 - 29.53: 1 29.53 - 59.02: 0 59.02 - 88.50: 1 88.50 - 117.99: 12495 117.99 - 147.48: 10489 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 2.520 nonbonded pdb=" OD1 ASP V 17 " pdb=" N ARG V 18 " model vdw 2.093 2.520 nonbonded pdb=" O HIS C 100B" pdb=" ND1 HIS C 100B" model vdw 2.161 2.520 nonbonded pdb=" OD1 ASP N 17 " pdb=" N ARG N 18 " model vdw 2.185 2.520 nonbonded pdb=" N GLN A 105 " pdb=" OE1 GLN A 105 " model vdw 2.199 2.520 ... (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 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: 0.760 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: 3.370 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 46.190 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.670 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.916 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 204 average time/residue: 0.2862 time to fit residues: 88.2107 Evaluate side-chains 205 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1818 time to fit residues: 3.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 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** E 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16912 Z= 0.231 Angle : 0.552 9.645 22986 Z= 0.293 Chirality : 0.043 0.165 2485 Planarity : 0.004 0.057 2933 Dihedral : 4.422 18.059 2330 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.60 % Allowed : 12.76 % Favored : 84.64 % 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: 0.29 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.32 (0.18), residues: 936 loop : 0.22 (0.19), residues: 1159 *********************** 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 273 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 34 residues processed: 252 average time/residue: 0.2871 time to fit residues: 110.1412 Evaluate side-chains 236 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1962 time to fit residues: 14.0541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 186 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Q 35 HIS Q 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16912 Z= 0.217 Angle : 0.522 8.215 22986 Z= 0.276 Chirality : 0.042 0.196 2485 Planarity : 0.004 0.052 2933 Dihedral : 4.318 18.718 2330 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.10 % Allowed : 14.25 % Favored : 84.64 % 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: 0.36 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.44 (0.18), residues: 936 loop : 0.19 (0.19), residues: 1159 *********************** 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 254 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.983 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 250 average time/residue: 0.2764 time to fit residues: 106.2039 Evaluate side-chains 219 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1803 time to fit residues: 6.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN C 97 HIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS V 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16912 Z= 0.238 Angle : 0.531 8.381 22986 Z= 0.280 Chirality : 0.042 0.205 2485 Planarity : 0.004 0.049 2933 Dihedral : 4.310 17.634 2330 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.32 % Allowed : 13.54 % Favored : 84.14 % 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: 0.30 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.37 (0.17), residues: 963 loop : 0.18 (0.20), residues: 1132 *********************** 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 265 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.109 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 252 average time/residue: 0.2773 time to fit residues: 107.2463 Evaluate side-chains 231 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1706 time to fit residues: 11.0665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16912 Z= 0.193 Angle : 0.516 8.667 22986 Z= 0.272 Chirality : 0.042 0.221 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.216 18.275 2330 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.72 % Allowed : 14.97 % Favored : 84.31 % 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: 0.35 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.42 (0.17), residues: 963 loop : 0.18 (0.19), residues: 1132 *********************** 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 226 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 2.049 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 223 average time/residue: 0.2691 time to fit residues: 92.2217 Evaluate side-chains 204 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1624 time to fit residues: 4.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 48 optimal weight: 40.0000 chunk 198 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS Q 35 HIS Q 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 16912 Z= 0.551 Angle : 0.693 8.471 22986 Z= 0.369 Chirality : 0.047 0.236 2485 Planarity : 0.005 0.045 2933 Dihedral : 5.016 22.940 2330 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.93 % Allowed : 14.64 % Favored : 83.43 % 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: -0.24 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.12 (0.16), residues: 1062 loop : -0.35 (0.20), residues: 1033 *********************** 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 224 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 2.045 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 217 average time/residue: 0.2890 time to fit residues: 95.3472 Evaluate side-chains 203 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1810 time to fit residues: 9.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 97 HIS M 97 HIS O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.004 0.032 16912 Z= 0.256 Angle : 0.563 9.108 22986 Z= 0.298 Chirality : 0.043 0.287 2485 Planarity : 0.004 0.045 2933 Dihedral : 4.613 20.490 2330 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.05 % Allowed : 15.58 % Favored : 83.37 % 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 (0.18), residues: 936 loop : -0.19 (0.19), residues: 1159 *********************** REFINEMENT MACRO_CYCLE 7 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 224 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 2.098 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 215 average time/residue: 0.2743 time to fit residues: 90.8649 Evaluate side-chains 199 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1895 time to fit residues: 5.7427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 118 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 24 ASN C 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16912 Z= 0.161 Angle : 0.523 9.182 22986 Z= 0.275 Chirality : 0.042 0.300 2485 Planarity : 0.003 0.045 2933 Dihedral : 4.227 16.404 2330 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.27 % Allowed : 15.69 % Favored : 83.04 % 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: 0.18 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.36 (0.17), residues: 963 loop : 0.01 (0.19), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 8 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 238 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 2.094 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 227 average time/residue: 0.2795 time to fit residues: 97.7260 Evaluate side-chains 201 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2032 time to fit residues: 6.1461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 120 optimal weight: 0.0770 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS S 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16912 Z= 0.227 Angle : 0.552 9.252 22986 Z= 0.291 Chirality : 0.043 0.278 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.312 18.449 2330 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.44 % Allowed : 16.85 % Favored : 82.71 % 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: 0.20 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 963 loop : -0.00 (0.19), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 9 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 202 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 2.164 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 198 average time/residue: 0.2867 time to fit residues: 87.1765 Evaluate side-chains 190 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1832 time to fit residues: 3.5570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16912 Z= 0.266 Angle : 0.577 9.357 22986 Z= 0.303 Chirality : 0.043 0.280 2485 Planarity : 0.004 0.046 2933 Dihedral : 4.420 19.499 2330 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.44 % Allowed : 17.24 % Favored : 82.32 % 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: 0.15 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.37 (0.17), residues: 963 loop : -0.04 (0.19), residues: 1132 ********************** REFINEMENT MACRO_CYCLE 10 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 199 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.692 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 195 average time/residue: 0.2820 time to fit residues: 85.4740 Evaluate side-chains 191 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2313 time to fit residues: 4.6650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 162 optimal weight: 0.0060 chunk 68 optimal weight: 0.0020 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100BHIS C 81 GLN ** C 100BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS O 97 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092599 restraints weight = 30737.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094702 restraints weight = 19487.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096110 restraints weight = 14278.301| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16912 Z= 0.151 Angle : 0.534 9.518 22986 Z= 0.280 Chirality : 0.042 0.289 2485 Planarity : 0.004 0.048 2933 Dihedral : 4.160 20.598 2330 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.17 % Allowed : 17.57 % Favored : 82.27 % 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: 0.33 (0.19), residues: 2095 helix: None (None), residues: 0 sheet: 0.49 (0.17), residues: 963 loop : 0.08 (0.19), residues: 1132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.21 seconds wall clock time: 54 minutes 55.98 seconds (3295.98 seconds total)