Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 03:52:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/08_2023/6ofg_20045.pdb" } resolution = 2.9 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= 0.001 sd= 0.010 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: 3 Type Number sf(0) Gaussians C 6930 2.51 5 N 1818 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 80": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10980 Number of models: 1 Model: "" Number of chains: 18 Chain: "P" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 6.03, per 1000 atoms: 0.55 Number of scatterers: 10980 At special positions: 0 Unit cell: (90.915, 90.915, 147.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2232 8.00 N 1818 7.00 C 6930 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 80 No H-bonds generated for 'chain 'L' and resid 78 through 80' Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 80 No H-bonds generated for 'chain 'M' and resid 78 through 80' Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 80 No H-bonds generated for 'chain 'N' and resid 78 through 80' Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 80 No H-bonds generated for 'chain 'O' and resid 78 through 80' Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' 900 hydrogen bonds defined for protein. 2700 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: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1962 1.29 - 1.35: 1674 1.35 - 1.41: 1087 1.41 - 1.48: 1689 1.48 - 1.54: 4766 Bond restraints: 11178 Sorted by residual: bond pdb=" CB GLU O 53 " pdb=" CG GLU O 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU K 53 " pdb=" CG GLU K 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLU Q 53 " pdb=" CG GLU Q 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 ... (remaining 11173 not shown) Histogram of bond angle deviations from ideal: 102.69 - 108.91: 639 108.91 - 115.13: 6183 115.13 - 121.36: 6049 121.36 - 127.58: 2249 127.58 - 133.80: 90 Bond angle restraints: 15210 Sorted by residual: angle pdb=" C VAL M 20 " pdb=" N ASP M 21 " pdb=" CA ASP M 21 " ideal model delta sigma weight residual 121.81 117.26 4.55 1.83e+00 2.99e-01 6.17e+00 angle pdb=" C VAL H 20 " pdb=" N ASP H 21 " pdb=" CA ASP H 21 " ideal model delta sigma weight residual 121.81 117.29 4.52 1.83e+00 2.99e-01 6.09e+00 angle pdb=" C VAL O 20 " pdb=" N ASP O 21 " pdb=" CA ASP O 21 " ideal model delta sigma weight residual 121.81 117.30 4.51 1.83e+00 2.99e-01 6.07e+00 angle pdb=" C VAL G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 angle pdb=" C VAL R 20 " pdb=" N ASP R 21 " pdb=" CA ASP R 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 ... (remaining 15205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 6534 14.84 - 29.68: 180 29.68 - 44.52: 54 44.52 - 59.37: 0 59.37 - 74.21: 18 Dihedral angle restraints: 6786 sinusoidal: 2592 harmonic: 4194 Sorted by residual: dihedral pdb=" CA GLY N 19 " pdb=" C GLY N 19 " pdb=" N VAL N 20 " pdb=" CA VAL N 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY H 19 " pdb=" C GLY H 19 " pdb=" N VAL H 20 " pdb=" CA VAL H 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY D 19 " pdb=" C GLY D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 425 0.020 - 0.040: 694 0.040 - 0.059: 305 0.059 - 0.079: 184 0.079 - 0.099: 120 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PRO D 38 " pdb=" N PRO D 38 " pdb=" C PRO D 38 " pdb=" CB PRO D 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO L 38 " pdb=" N PRO L 38 " pdb=" C PRO L 38 " pdb=" CB PRO L 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO B 41 " pdb=" N PRO B 41 " pdb=" C PRO B 41 " pdb=" CB PRO B 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.38e-01 ... (remaining 1725 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL A 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL N 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL N 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP N 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 20 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C VAL G 20 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL G 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 21 " -0.008 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3286 2.79 - 3.32: 10703 3.32 - 3.85: 18136 3.85 - 4.37: 23422 4.37 - 4.90: 38800 Nonbonded interactions: 94347 Sorted by model distance: nonbonded pdb=" OD1 ASP K 17 " pdb=" OH TYR K 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP Q 17 " pdb=" OH TYR Q 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP G 17 " pdb=" OH TYR G 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP C 17 " pdb=" OH TYR C 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.263 2.440 ... (remaining 94342 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' } 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: 0.980 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: 4.460 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.200 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.008 0.040 11178 Z= 0.480 Angle : 0.750 4.546 15210 Z= 0.406 Chirality : 0.043 0.099 1728 Planarity : 0.005 0.030 1998 Dihedral : 10.039 74.208 4050 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.00 % 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: -6.09 (0.10), residues: 1368 helix: -3.76 (0.06), residues: 1170 sheet: None (None), residues: 0 loop : -3.57 (0.31), residues: 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 1.0014 time to fit residues: 386.4624 Evaluate side-chains 239 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN Q 78 ASN R 61 GLN K 61 GLN K 63 ASN K 77 GLN K 78 ASN L 55 ASN L 61 GLN L 77 GLN M 55 ASN M 61 GLN N 55 ASN N 61 GLN O 55 ASN O 61 GLN F 61 GLN F 78 ASN G 61 GLN G 77 GLN G 78 ASN H 61 GLN H 78 ASN I 61 GLN J 61 GLN J 78 ASN A 59 ASN A 61 GLN B 61 GLN C 61 GLN D 61 GLN E 61 GLN E 63 ASN E 77 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 11178 Z= 0.143 Angle : 0.456 3.530 15210 Z= 0.257 Chirality : 0.033 0.106 1728 Planarity : 0.005 0.027 1998 Dihedral : 4.137 20.754 1512 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 3.59 % 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: -0.64 (0.18), residues: 1368 helix: 0.00 (0.11), residues: 1224 sheet: None (None), residues: 0 loop : -3.13 (0.45), residues: 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 268 time to evaluate : 1.158 Fit side-chains outliers start: 42 outliers final: 22 residues processed: 287 average time/residue: 0.8650 time to fit residues: 274.9858 Evaluate side-chains 248 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 6 average time/residue: 0.1846 time to fit residues: 3.3104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN K 77 GLN L 61 GLN L 77 GLN M 61 GLN O 61 GLN F 61 GLN F 78 ASN G 61 GLN G 77 GLN G 78 ASN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN J 61 GLN A 78 ASN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 61 GLN E 77 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.151 Angle : 0.432 3.389 15210 Z= 0.237 Chirality : 0.033 0.102 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.703 18.602 1512 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 3.85 % 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: 2.33 (0.21), residues: 1368 helix: 2.02 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.81 (0.49), residues: 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 1.320 Fit side-chains outliers start: 45 outliers final: 28 residues processed: 288 average time/residue: 0.9394 time to fit residues: 297.0986 Evaluate side-chains 269 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.3907 time to fit residues: 5.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 32 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: P 61 GLN Q 61 GLN K 63 ASN K 77 GLN L 24 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN F 61 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 77 GLN J 61 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 11178 Z= 0.151 Angle : 0.418 3.567 15210 Z= 0.227 Chirality : 0.033 0.102 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.577 17.594 1512 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 3.85 % 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: 3.44 (0.22), residues: 1368 helix: 2.76 (0.14), residues: 1224 sheet: None (None), residues: 0 loop : -2.47 (0.51), residues: 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 279 average time/residue: 0.9152 time to fit residues: 280.8482 Evaluate side-chains 268 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 4 average time/residue: 0.1586 time to fit residues: 2.6016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 11178 Z= 0.144 Angle : 0.406 3.316 15210 Z= 0.220 Chirality : 0.033 0.116 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.433 16.371 1512 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 3.76 % 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: 3.94 (0.22), residues: 1368 helix: 3.11 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.49 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 241 time to evaluate : 0.980 Fit side-chains outliers start: 44 outliers final: 36 residues processed: 276 average time/residue: 0.9225 time to fit residues: 279.8538 Evaluate side-chains 266 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 0.8356 time to fit residues: 6.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN M 61 GLN O 61 GLN F 77 GLN F 78 ASN G 61 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.124 Angle : 0.387 3.288 15210 Z= 0.210 Chirality : 0.032 0.099 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.322 15.162 1512 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 3.93 % 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: 4.39 (0.22), residues: 1368 helix: 3.41 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.46 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 244 time to evaluate : 1.287 Fit side-chains outliers start: 46 outliers final: 39 residues processed: 284 average time/residue: 0.9251 time to fit residues: 289.3488 Evaluate side-chains 270 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 0.4489 time to fit residues: 4.4206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN L 61 GLN L 77 GLN M 61 GLN O 61 GLN F 77 GLN G 61 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 11178 Z= 0.149 Angle : 0.409 3.837 15210 Z= 0.221 Chirality : 0.033 0.129 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.321 14.330 1512 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 4.02 % 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: 4.48 (0.22), residues: 1368 helix: 3.48 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.54 (0.53), residues: 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.174 Fit side-chains outliers start: 47 outliers final: 39 residues processed: 282 average time/residue: 0.9251 time to fit residues: 287.1796 Evaluate side-chains 273 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 234 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 3 average time/residue: 0.6790 time to fit residues: 3.9807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN M 61 GLN N 61 GLN F 61 GLN F 77 GLN F 78 ASN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN D 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 11178 Z= 0.177 Angle : 0.428 4.005 15210 Z= 0.229 Chirality : 0.034 0.146 1728 Planarity : 0.003 0.026 1998 Dihedral : 3.361 14.268 1512 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 4.02 % 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: 4.49 (0.22), residues: 1368 helix: 3.49 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 1.184 Fit side-chains outliers start: 47 outliers final: 40 residues processed: 285 average time/residue: 0.9067 time to fit residues: 285.4754 Evaluate side-chains 282 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 5 average time/residue: 0.4832 time to fit residues: 4.4445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN M 61 GLN N 61 GLN F 61 GLN F 77 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN D 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 11178 Z= 0.163 Angle : 0.417 3.912 15210 Z= 0.225 Chirality : 0.033 0.151 1728 Planarity : 0.003 0.025 1998 Dihedral : 3.326 13.780 1512 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 3.68 % 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: 4.61 (0.22), residues: 1368 helix: 3.57 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.51 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 1.262 Fit side-chains outliers start: 43 outliers final: 38 residues processed: 280 average time/residue: 0.8883 time to fit residues: 275.2751 Evaluate side-chains 275 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 0.1429 time to fit residues: 2.3651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.0170 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN L 61 GLN M 61 GLN O 61 GLN G 61 GLN G 77 GLN H 61 GLN H 78 ASN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 11178 Z= 0.112 Angle : 0.384 3.438 15210 Z= 0.208 Chirality : 0.032 0.145 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.157 12.514 1512 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.16 % 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: 4.95 (0.22), residues: 1368 helix: 3.80 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.48 (0.52), residues: 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 36 residues processed: 283 average time/residue: 0.8919 time to fit residues: 278.6388 Evaluate side-chains 267 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 35 residues processed: 1 average time/residue: 0.2346 time to fit residues: 2.1010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN R 61 GLN K 61 GLN L 61 GLN M 61 GLN N 61 GLN O 61 GLN F 61 GLN F 77 GLN G 61 GLN G 77 GLN H 61 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN J 61 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092305 restraints weight = 15782.215| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.70 r_work: 0.2948 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 11178 Z= 0.303 Angle : 0.507 5.019 15210 Z= 0.271 Chirality : 0.038 0.191 1728 Planarity : 0.003 0.023 1998 Dihedral : 3.563 15.784 1512 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.16 % 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: 4.39 (0.21), residues: 1368 helix: 3.41 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.49 (0.52), residues: 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4536.18 seconds wall clock time: 82 minutes 41.44 seconds (4961.44 seconds total)