Starting phenix.real_space_refine on Sat Dec 9 10:29:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/12_2023/6a7f_6993.pdb" } resolution = 3.4 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= 0.000 sd= 0.007 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 30 5.16 5 C 7050 2.51 5 N 1740 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "G" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "H" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "L" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Q" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "R" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "S" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "U" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "V" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "W" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "X" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "Z" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "a" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "b" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "c" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "d" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 6.05, per 1000 atoms: 0.56 Number of scatterers: 10830 At special positions: 0 Unit cell: (76.7, 76.7, 165.1, 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 30 16.00 O 2010 8.00 N 1740 7.00 C 7050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.40 Conformation dependent library (CDL) restraints added in 2.0 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 95.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 4.020A pdb=" N ALA A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 30 - end of helix removed outlier: 4.020A pdb=" N ALA B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Proline residue: C 30 - end of helix removed outlier: 4.021A pdb=" N ALA C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 4.021A pdb=" N ALA D 38 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) Proline residue: E 30 - end of helix removed outlier: 4.021A pdb=" N ALA E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Proline residue: F 30 - end of helix removed outlier: 4.020A pdb=" N ALA F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) Proline residue: G 30 - end of helix removed outlier: 4.022A pdb=" N ALA G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Proline residue: H 30 - end of helix removed outlier: 4.021A pdb=" N ALA H 38 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS H 46 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 4.021A pdb=" N ALA I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 43 " --> pdb=" O GLY I 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Proline residue: J 30 - end of helix removed outlier: 4.021A pdb=" N ALA J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) Proline residue: K 30 - end of helix removed outlier: 4.021A pdb=" N ALA K 38 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 46 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) Proline residue: L 30 - end of helix removed outlier: 4.022A pdb=" N ALA L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG L 43 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP M 23 " --> pdb=" O THR M 19 " (cutoff:3.500A) Proline residue: M 30 - end of helix removed outlier: 4.021A pdb=" N ALA M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS M 46 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP N 23 " --> pdb=" O THR N 19 " (cutoff:3.500A) Proline residue: N 30 - end of helix removed outlier: 4.020A pdb=" N ALA N 38 " --> pdb=" O THR N 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE N 42 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL N 53 " --> pdb=" O SER N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP O 23 " --> pdb=" O THR O 19 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 4.022A pdb=" N ALA O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG O 43 " --> pdb=" O GLY O 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS O 46 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL O 53 " --> pdb=" O SER O 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Proline residue: P 30 - end of helix removed outlier: 4.021A pdb=" N ALA P 38 " --> pdb=" O THR P 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE P 42 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG P 43 " --> pdb=" O GLY P 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS P 46 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL P 53 " --> pdb=" O SER P 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Q 23 " --> pdb=" O THR Q 19 " (cutoff:3.500A) Proline residue: Q 30 - end of helix removed outlier: 4.022A pdb=" N ALA Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG Q 43 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS Q 46 " --> pdb=" O ILE Q 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Q 53 " --> pdb=" O SER Q 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP R 23 " --> pdb=" O THR R 19 " (cutoff:3.500A) Proline residue: R 30 - end of helix removed outlier: 4.021A pdb=" N ALA R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL R 53 " --> pdb=" O SER R 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP S 23 " --> pdb=" O THR S 19 " (cutoff:3.500A) Proline residue: S 30 - end of helix removed outlier: 4.021A pdb=" N ALA S 38 " --> pdb=" O THR S 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG S 43 " --> pdb=" O GLY S 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP T 23 " --> pdb=" O THR T 19 " (cutoff:3.500A) Proline residue: T 30 - end of helix removed outlier: 4.021A pdb=" N ALA T 38 " --> pdb=" O THR T 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE T 42 " --> pdb=" O ALA T 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG T 43 " --> pdb=" O GLY T 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) Proline residue: U 30 - end of helix removed outlier: 4.021A pdb=" N ALA U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 42 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG U 43 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS U 46 " --> pdb=" O ILE U 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL U 53 " --> pdb=" O SER U 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP V 23 " --> pdb=" O THR V 19 " (cutoff:3.500A) Proline residue: V 30 - end of helix removed outlier: 4.022A pdb=" N ALA V 38 " --> pdb=" O THR V 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE V 42 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG V 43 " --> pdb=" O GLY V 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS V 46 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL V 53 " --> pdb=" O SER V 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP W 23 " --> pdb=" O THR W 19 " (cutoff:3.500A) Proline residue: W 30 - end of helix removed outlier: 4.021A pdb=" N ALA W 38 " --> pdb=" O THR W 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE W 42 " --> pdb=" O ALA W 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS W 46 " --> pdb=" O ILE W 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL W 53 " --> pdb=" O SER W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP X 23 " --> pdb=" O THR X 19 " (cutoff:3.500A) Proline residue: X 30 - end of helix removed outlier: 4.022A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE X 42 " --> pdb=" O ALA X 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG X 43 " --> pdb=" O GLY X 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS X 46 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL X 53 " --> pdb=" O SER X 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Y 23 " --> pdb=" O THR Y 19 " (cutoff:3.500A) Proline residue: Y 30 - end of helix removed outlier: 4.021A pdb=" N ALA Y 38 " --> pdb=" O THR Y 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Y 43 " --> pdb=" O GLY Y 39 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Y 46 " --> pdb=" O ILE Y 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP Z 23 " --> pdb=" O THR Z 19 " (cutoff:3.500A) Proline residue: Z 30 - end of helix removed outlier: 4.021A pdb=" N ALA Z 38 " --> pdb=" O THR Z 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Z 42 " --> pdb=" O ALA Z 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Z 43 " --> pdb=" O GLY Z 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS Z 46 " --> pdb=" O ILE Z 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 53 removed outlier: 3.629A pdb=" N ASP a 23 " --> pdb=" O THR a 19 " (cutoff:3.500A) Proline residue: a 30 - end of helix removed outlier: 4.020A pdb=" N ALA a 38 " --> pdb=" O THR a 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 42 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS a 46 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL a 53 " --> pdb=" O SER a 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP b 23 " --> pdb=" O THR b 19 " (cutoff:3.500A) Proline residue: b 30 - end of helix removed outlier: 4.020A pdb=" N ALA b 38 " --> pdb=" O THR b 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 53 " --> pdb=" O SER b 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP c 23 " --> pdb=" O THR c 19 " (cutoff:3.500A) Proline residue: c 30 - end of helix removed outlier: 4.020A pdb=" N ALA c 38 " --> pdb=" O THR c 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE c 42 " --> pdb=" O ALA c 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL c 53 " --> pdb=" O SER c 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP d 23 " --> pdb=" O THR d 19 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 4.021A pdb=" N ALA d 38 " --> pdb=" O THR d 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE d 42 " --> pdb=" O ALA d 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS d 46 " --> pdb=" O ILE d 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL d 53 " --> pdb=" O SER d 49 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2880 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: 2.95 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3199 1.33 - 1.45: 1403 1.45 - 1.56: 6318 1.56 - 1.67: 0 1.67 - 1.79: 60 Bond restraints: 10980 Sorted by residual: bond pdb=" CB VAL X 32 " pdb=" CG2 VAL X 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB VAL M 32 " pdb=" CG2 VAL M 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL d 32 " pdb=" CG2 VAL d 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL H 32 " pdb=" CG2 VAL H 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL c 32 " pdb=" CG2 VAL c 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 ... (remaining 10975 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.30: 180 106.30 - 113.19: 6759 113.19 - 120.09: 3934 120.09 - 126.99: 3947 126.99 - 133.89: 120 Bond angle restraints: 14940 Sorted by residual: angle pdb=" N TRP I 29 " pdb=" CA TRP I 29 " pdb=" C TRP I 29 " ideal model delta sigma weight residual 113.45 117.78 -4.33 1.39e+00 5.18e-01 9.70e+00 angle pdb=" N TRP F 29 " pdb=" CA TRP F 29 " pdb=" C TRP F 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.68e+00 angle pdb=" N TRP U 29 " pdb=" CA TRP U 29 " pdb=" C TRP U 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.66e+00 angle pdb=" N TRP J 29 " pdb=" CA TRP J 29 " pdb=" C TRP J 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.63e+00 angle pdb=" N TRP a 29 " pdb=" CA TRP a 29 " pdb=" C TRP a 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.62e+00 ... (remaining 14935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 6120 14.33 - 28.65: 420 28.65 - 42.98: 30 42.98 - 57.30: 0 57.30 - 71.63: 30 Dihedral angle restraints: 6600 sinusoidal: 2430 harmonic: 4170 Sorted by residual: dihedral pdb=" CA THR G 7 " pdb=" C THR G 7 " pdb=" N ASN G 8 " pdb=" CA ASN G 8 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR R 7 " pdb=" C THR R 7 " pdb=" N ASN R 8 " pdb=" CA ASN R 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR C 7 " pdb=" C THR C 7 " pdb=" N ASN C 8 " pdb=" CA ASN C 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1023 0.042 - 0.083: 614 0.083 - 0.125: 209 0.125 - 0.166: 104 0.166 - 0.208: 30 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA TRP I 29 " pdb=" N TRP I 29 " pdb=" C TRP I 29 " pdb=" CB TRP I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TRP Q 29 " pdb=" N TRP Q 29 " pdb=" C TRP Q 29 " pdb=" CB TRP Q 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP d 29 " pdb=" N TRP d 29 " pdb=" C TRP d 29 " pdb=" CB TRP d 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1977 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL T 41 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C VAL T 41 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL T 41 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE T 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL W 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL W 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE W 42 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL b 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL b 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE b 42 " -0.011 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3091 2.80 - 3.32: 11247 3.32 - 3.85: 18366 3.85 - 4.37: 20225 4.37 - 4.90: 35192 Nonbonded interactions: 88121 Sorted by model distance: nonbonded pdb=" NZ LYS C 46 " pdb=" O LYS I 51 " model vdw 2.271 2.520 nonbonded pdb=" NZ LYS W 46 " pdb=" O VAL c 53 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS T 46 " pdb=" O VAL U 53 " model vdw 2.328 2.520 nonbonded pdb=" NZ LYS O 46 " pdb=" O VAL P 53 " model vdw 2.332 2.520 nonbonded pdb=" O ALA a 13 " pdb=" OG SER a 16 " model vdw 2.339 2.440 ... (remaining 88116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 3.330 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.510 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.150 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.014 0.064 10980 Z= 0.903 Angle : 1.172 6.672 14940 Z= 0.615 Chirality : 0.064 0.208 1980 Planarity : 0.008 0.044 1740 Dihedral : 11.202 71.631 3840 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.18), residues: 1350 helix: -1.19 (0.11), residues: 1320 sheet: None (None), residues: 0 loop : -0.50 (0.01), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 29 PHE 0.008 0.003 PHE Y 48 TYR 0.003 0.001 TYR G 9 ARG 0.006 0.002 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 0.2393 time to fit residues: 270.6092 Evaluate side-chains 649 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN C 27 GLN D 27 GLN F 27 GLN J 27 GLN L 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10980 Z= 0.209 Angle : 0.580 7.535 14940 Z= 0.303 Chirality : 0.040 0.129 1980 Planarity : 0.005 0.032 1740 Dihedral : 4.333 12.061 1440 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.90 % Allowed : 20.33 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1350 helix: 0.56 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 2.23 (0.27), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 29 PHE 0.010 0.001 PHE Q 48 TYR 0.007 0.001 TYR F 9 ARG 0.002 0.001 ARG N 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 814 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 33 residues processed: 819 average time/residue: 0.2249 time to fit residues: 254.5202 Evaluate side-chains 752 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 719 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1024 time to fit residues: 7.7531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10980 Z= 0.224 Angle : 0.580 6.841 14940 Z= 0.298 Chirality : 0.041 0.135 1980 Planarity : 0.004 0.030 1740 Dihedral : 4.117 11.447 1440 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.28 % Allowed : 24.55 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1350 helix: 1.06 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.03 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 29 PHE 0.012 0.001 PHE Q 48 TYR 0.010 0.001 TYR H 9 ARG 0.003 0.000 ARG Q 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 761 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 765 average time/residue: 0.2160 time to fit residues: 229.9687 Evaluate side-chains 744 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 720 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1056 time to fit residues: 6.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 27 GLN D 27 GLN F 27 GLN I 27 GLN O 8 ASN S 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10980 Z= 0.220 Angle : 0.581 6.951 14940 Z= 0.300 Chirality : 0.042 0.141 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.004 11.417 1440 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.44 % Allowed : 27.97 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1350 helix: 1.26 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.50 (0.48), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 29 PHE 0.011 0.001 PHE Q 48 TYR 0.006 0.001 TYR K 9 ARG 0.003 0.000 ARG c 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 756 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 757 average time/residue: 0.2112 time to fit residues: 223.7656 Evaluate side-chains 744 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 722 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1253 time to fit residues: 6.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 8 ASN F 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10980 Z= 0.211 Angle : 0.592 8.456 14940 Z= 0.303 Chirality : 0.042 0.161 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.958 12.883 1440 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.11 % Allowed : 29.76 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1350 helix: 1.33 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.50 (0.48), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 29 PHE 0.017 0.001 PHE U 48 TYR 0.012 0.001 TYR b 9 ARG 0.003 0.000 ARG c 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 746 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 753 average time/residue: 0.2151 time to fit residues: 226.4730 Evaluate side-chains 730 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 716 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0967 time to fit residues: 4.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0000 chunk 60 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN F 27 GLN I 8 ASN Q 27 GLN R 27 GLN S 27 GLN W 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10980 Z= 0.249 Angle : 0.598 7.301 14940 Z= 0.311 Chirality : 0.043 0.191 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.967 12.660 1440 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.03 % Allowed : 31.95 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1350 helix: 1.33 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.37 (0.49), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 29 PHE 0.023 0.001 PHE U 48 TYR 0.010 0.001 TYR d 9 ARG 0.004 0.000 ARG S 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 724 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 728 average time/residue: 0.2168 time to fit residues: 221.4907 Evaluate side-chains 718 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 701 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1026 time to fit residues: 4.8173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN Q 27 GLN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10980 Z= 0.287 Angle : 0.625 6.821 14940 Z= 0.325 Chirality : 0.044 0.203 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.013 12.063 1440 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 1.95 % Allowed : 33.58 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1350 helix: 1.31 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.11 (0.58), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 29 PHE 0.023 0.002 PHE U 48 TYR 0.008 0.001 TYR X 9 ARG 0.003 0.001 ARG S 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 704 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 709 average time/residue: 0.2149 time to fit residues: 213.3975 Evaluate side-chains 703 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 688 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1154 time to fit residues: 4.5755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN F 27 GLN Q 27 GLN R 27 GLN S 27 GLN V 27 GLN W 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10980 Z= 0.213 Angle : 0.614 6.916 14940 Z= 0.317 Chirality : 0.043 0.191 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.995 11.777 1440 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 1.22 % Allowed : 33.98 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1350 helix: 1.36 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.22 (0.61), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 29 PHE 0.019 0.001 PHE U 48 TYR 0.008 0.001 TYR a 9 ARG 0.003 0.000 ARG S 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 745 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 747 average time/residue: 0.2243 time to fit residues: 234.4140 Evaluate side-chains 732 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 721 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1067 time to fit residues: 3.6880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN Q 27 GLN R 27 GLN S 27 GLN V 27 GLN W 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10980 Z= 0.231 Angle : 0.630 7.516 14940 Z= 0.326 Chirality : 0.044 0.207 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.003 14.043 1440 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.65 % Allowed : 36.18 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1350 helix: 1.37 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.62 (0.59), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 29 PHE 0.014 0.001 PHE b 48 TYR 0.008 0.001 TYR Y 9 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 727 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 729 average time/residue: 0.2166 time to fit residues: 220.3489 Evaluate side-chains 717 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 711 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0995 time to fit residues: 2.7919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN I 8 ASN Q 27 GLN R 27 GLN S 27 GLN V 27 GLN W 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10980 Z= 0.224 Angle : 0.646 7.642 14940 Z= 0.337 Chirality : 0.044 0.201 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.083 13.868 1440 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.57 % Allowed : 36.83 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1350 helix: 1.33 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.11 (0.61), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 29 PHE 0.013 0.001 PHE b 48 TYR 0.008 0.001 TYR G 9 ARG 0.004 0.001 ARG F 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 727 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 728 average time/residue: 0.2149 time to fit residues: 218.5178 Evaluate side-chains 719 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 715 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1760 time to fit residues: 2.7092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 27 GLN R 27 GLN W 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079378 restraints weight = 21120.597| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.18 r_work: 0.3192 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10980 Z= 0.228 Angle : 0.652 7.428 14940 Z= 0.338 Chirality : 0.044 0.201 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.081 14.052 1440 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.33 % Allowed : 37.80 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1350 helix: 1.31 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.21 (0.64), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 29 PHE 0.012 0.001 PHE b 48 TYR 0.007 0.001 TYR H 9 ARG 0.004 0.000 ARG F 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.02 seconds wall clock time: 66 minutes 20.62 seconds (3980.62 seconds total)