Starting phenix.real_space_refine (version: dev) on Sun Feb 19 23:24:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2023/7m30_23640.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1676 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B ARG 89": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "N PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9191 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 78} Chain: "C" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 893 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 775 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 94} Chain breaks: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.34, per 1000 atoms: 0.58 Number of scatterers: 9191 At special positions: 0 Unit cell: (83.85, 142.975, 145.125, 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 47 16.00 O 1776 8.00 N 1591 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 Links applied NAG-ASN " NAG D 300 " - " ASN D 201 " " NAG E 200 " - " ASN E 81 " Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 22 sheets defined 20.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.715A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.816A pdb=" N GLY B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.668A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 5.394A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 83 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 92 through 97 removed outlier: 5.667A pdb=" N SER C 95 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.837A pdb=" N ARG D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.995A pdb=" N LYS D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 110 " --> pdb=" O TRP D 106 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 Proline residue: D 126 - end of helix removed outlier: 3.811A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 4.022A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.794A pdb=" N VAL E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.730A pdb=" N ALA F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.570A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.600A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 154 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.596A pdb=" N LYS C 47 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 3.847A pdb=" N GLU D 177 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 118 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 71 through 78 removed outlier: 6.669A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 88 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.297A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 13 396 hydrogen bonds defined for protein. 984 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: 2.54 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2990 1.34 - 1.47: 2486 1.47 - 1.60: 3862 1.60 - 1.73: 0 1.73 - 1.86: 64 Bond restraints: 9402 Sorted by residual: bond pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.27e-02 6.20e+03 1.02e+01 bond pdb=" C LEU L 94 " pdb=" O LEU L 94 " ideal model delta sigma weight residual 1.239 1.219 0.020 9.60e-03 1.09e+04 4.14e+00 bond pdb=" CA GLN N 89 " pdb=" C GLN N 89 " ideal model delta sigma weight residual 1.520 1.498 0.022 1.16e-02 7.43e+03 3.67e+00 bond pdb=" CG GLU D 101 " pdb=" CD GLU D 101 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ASN N 96 " pdb=" C ASN N 96 " ideal model delta sigma weight residual 1.524 1.500 0.023 1.29e-02 6.01e+03 3.27e+00 ... (remaining 9397 not shown) Histogram of bond angle deviations from ideal: 96.83 - 105.37: 199 105.37 - 113.91: 5161 113.91 - 122.46: 5747 122.46 - 131.00: 1620 131.00 - 139.54: 35 Bond angle restraints: 12762 Sorted by residual: angle pdb=" N ASN N 97 " pdb=" CA ASN N 97 " pdb=" C ASN N 97 " ideal model delta sigma weight residual 110.53 120.78 -10.25 1.32e+00 5.74e-01 6.03e+01 angle pdb=" N CYS B 154 " pdb=" CA CYS B 154 " pdb=" C CYS B 154 " ideal model delta sigma weight residual 108.99 119.31 -10.32 1.57e+00 4.06e-01 4.32e+01 angle pdb=" CA SER F 97 " pdb=" C SER F 97 " pdb=" N THR F 98 " ideal model delta sigma weight residual 119.63 114.61 5.02 8.10e-01 1.52e+00 3.85e+01 angle pdb=" N ASP B 157 " pdb=" CA ASP B 157 " pdb=" C ASP B 157 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" C ALA B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 127.00 139.54 -12.54 2.40e+00 1.74e-01 2.73e+01 ... (remaining 12757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5113 17.43 - 34.85: 378 34.85 - 52.27: 95 52.27 - 69.70: 21 69.70 - 87.12: 11 Dihedral angle restraints: 5618 sinusoidal: 2233 harmonic: 3385 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.95 44.05 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 53.60 39.40 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1007 0.064 - 0.128: 306 0.128 - 0.192: 67 0.192 - 0.256: 15 0.256 - 0.320: 4 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU M 69 " pdb=" CB LEU M 69 " pdb=" CD1 LEU M 69 " pdb=" CD2 LEU M 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN N 97 " pdb=" N ASN N 97 " pdb=" C ASN N 97 " pdb=" CB ASN N 97 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE G 75 " pdb=" CA ILE G 75 " pdb=" CG1 ILE G 75 " pdb=" CG2 ILE G 75 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1396 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.58e+01 pdb=" NE ARG H 71 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 86 " 0.092 9.50e-02 1.11e+02 5.32e-02 1.53e+01 pdb=" NE ARG C 86 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 86 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 86 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG C 86 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 22 " -0.081 9.50e-02 1.11e+02 4.79e-02 1.29e+01 pdb=" NE ARG E 22 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 22 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG E 22 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG E 22 " 0.017 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 19 2.35 - 2.99: 4874 2.99 - 3.62: 13982 3.62 - 4.26: 21094 4.26 - 4.90: 34664 Nonbonded interactions: 74633 Sorted by model distance: nonbonded pdb=" OD1 ASP F 95 " pdb=" O TYR F 100D" model vdw 1.711 3.040 nonbonded pdb=" OD1 ASP B 103 " pdb=" N ALA B 104 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS C 117 " pdb=" O ASP G 29 " model vdw 2.236 2.520 nonbonded pdb=" OG SER N 7 " pdb=" OG1 THR N 22 " model vdw 2.236 2.440 nonbonded pdb=" OE1 GLN F 3 " pdb=" OG SER F 25 " model vdw 2.246 2.440 ... (remaining 74628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5777 2.51 5 N 1591 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 17.790 Check model and map are aligned: 0.150 Process input model: 27.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 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 : 0.005 0.054 9402 Z= 0.350 Angle : 1.149 13.578 12762 Z= 0.640 Chirality : 0.067 0.320 1399 Planarity : 0.008 0.084 1643 Dihedral : 13.592 87.119 3409 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.94 (0.25), residues: 1141 helix: -1.66 (0.36), residues: 157 sheet: -0.07 (0.25), residues: 399 loop : -0.61 (0.27), residues: 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 545 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 550 average time/residue: 0.2978 time to fit residues: 209.1121 Evaluate side-chains 464 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 460 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0911 time to fit residues: 2.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN E 129 ASN F 64 GLN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 79 GLN L 89 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 9402 Z= 0.387 Angle : 0.890 12.838 12762 Z= 0.463 Chirality : 0.053 0.233 1399 Planarity : 0.006 0.055 1643 Dihedral : 6.093 34.530 1303 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 5.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.56 (0.25), residues: 1141 helix: -1.04 (0.37), residues: 153 sheet: 0.07 (0.26), residues: 392 loop : -0.38 (0.27), residues: 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 491 time to evaluate : 1.249 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: 59 outliers final: 39 residues processed: 507 average time/residue: 0.2832 time to fit residues: 184.0274 Evaluate side-chains 497 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 458 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.0875 time to fit residues: 7.7009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS C 99 ASN E 129 ASN F 31 ASN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5802 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 9402 Z= 0.280 Angle : 0.828 10.159 12762 Z= 0.425 Chirality : 0.050 0.164 1399 Planarity : 0.006 0.055 1643 Dihedral : 6.041 35.082 1303 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.47 (0.25), residues: 1141 helix: -0.77 (0.39), residues: 152 sheet: 0.05 (0.26), residues: 395 loop : -0.32 (0.27), residues: 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 486 time to evaluate : 1.048 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: 40 outliers final: 21 residues processed: 497 average time/residue: 0.2750 time to fit residues: 176.8798 Evaluate side-chains 479 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 458 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1011 time to fit residues: 5.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN F 31 ASN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 9402 Z= 0.283 Angle : 0.841 10.805 12762 Z= 0.425 Chirality : 0.050 0.172 1399 Planarity : 0.006 0.053 1643 Dihedral : 6.131 34.003 1303 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.38 (0.25), residues: 1141 helix: -0.54 (0.41), residues: 148 sheet: 0.27 (0.27), residues: 380 loop : -0.43 (0.27), residues: 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 472 time to evaluate : 1.124 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: 45 outliers final: 29 residues processed: 482 average time/residue: 0.2788 time to fit residues: 173.6320 Evaluate side-chains 479 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 450 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1205 time to fit residues: 7.1206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN F 31 ASN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 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 : 0.005 0.077 9402 Z= 0.318 Angle : 0.856 10.700 12762 Z= 0.432 Chirality : 0.051 0.183 1399 Planarity : 0.007 0.062 1643 Dihedral : 6.228 33.634 1303 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.47 (0.25), residues: 1141 helix: -0.69 (0.40), residues: 153 sheet: 0.27 (0.27), residues: 382 loop : -0.51 (0.27), residues: 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 457 time to evaluate : 1.104 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: 46 outliers final: 26 residues processed: 472 average time/residue: 0.2791 time to fit residues: 169.0929 Evaluate side-chains 464 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 438 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0961 time to fit residues: 6.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 9402 Z= 0.328 Angle : 0.887 11.172 12762 Z= 0.445 Chirality : 0.051 0.240 1399 Planarity : 0.007 0.065 1643 Dihedral : 6.361 33.545 1303 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.53 (0.25), residues: 1141 helix: -0.56 (0.40), residues: 153 sheet: 0.18 (0.27), residues: 383 loop : -0.57 (0.27), residues: 605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 447 time to evaluate : 1.117 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: 43 outliers final: 24 residues processed: 455 average time/residue: 0.2688 time to fit residues: 158.0256 Evaluate side-chains 461 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 437 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0864 time to fit residues: 5.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 37 GLN G 42 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 9402 Z= 0.336 Angle : 0.908 11.669 12762 Z= 0.454 Chirality : 0.054 0.517 1399 Planarity : 0.006 0.060 1643 Dihedral : 6.388 33.638 1303 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.65 (0.25), residues: 1141 helix: -0.56 (0.40), residues: 152 sheet: 0.12 (0.27), residues: 373 loop : -0.68 (0.26), residues: 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 446 time to evaluate : 1.172 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: 39 outliers final: 22 residues processed: 459 average time/residue: 0.2704 time to fit residues: 160.6361 Evaluate side-chains 456 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 434 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1094 time to fit residues: 5.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 9402 Z= 0.320 Angle : 0.925 11.521 12762 Z= 0.460 Chirality : 0.054 0.463 1399 Planarity : 0.007 0.107 1643 Dihedral : 6.375 34.352 1303 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.63 (0.26), residues: 1141 helix: -0.34 (0.41), residues: 151 sheet: 0.04 (0.27), residues: 373 loop : -0.66 (0.27), residues: 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 448 time to evaluate : 1.144 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: 30 outliers final: 20 residues processed: 454 average time/residue: 0.2667 time to fit residues: 156.6828 Evaluate side-chains 451 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 431 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0861 time to fit residues: 4.6588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 9402 Z= 0.311 Angle : 0.949 11.599 12762 Z= 0.471 Chirality : 0.053 0.302 1399 Planarity : 0.007 0.079 1643 Dihedral : 6.411 31.541 1303 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.69 (0.26), residues: 1141 helix: -0.28 (0.42), residues: 148 sheet: -0.12 (0.27), residues: 392 loop : -0.65 (0.27), residues: 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 446 time to evaluate : 1.114 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: 24 outliers final: 14 residues processed: 449 average time/residue: 0.2745 time to fit residues: 159.0155 Evaluate side-chains 452 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 438 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1167 time to fit residues: 4.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.0770 chunk 102 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9402 Z= 0.290 Angle : 0.947 11.364 12762 Z= 0.471 Chirality : 0.052 0.263 1399 Planarity : 0.007 0.110 1643 Dihedral : 6.414 30.655 1303 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.73 (0.26), residues: 1141 helix: -0.24 (0.42), residues: 148 sheet: -0.07 (0.27), residues: 375 loop : -0.75 (0.26), residues: 618 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 437 time to evaluate : 1.077 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: 12 outliers final: 5 residues processed: 440 average time/residue: 0.2705 time to fit residues: 153.3810 Evaluate side-chains 433 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 428 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1780 time to fit residues: 2.7596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 91 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091781 restraints weight = 30542.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094775 restraints weight = 17455.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096806 restraints weight = 11333.475| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9402 Z= 0.261 Angle : 0.948 11.839 12762 Z= 0.466 Chirality : 0.052 0.269 1399 Planarity : 0.007 0.077 1643 Dihedral : 6.199 28.684 1303 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.68 (0.26), residues: 1141 helix: -0.24 (0.43), residues: 148 sheet: -0.08 (0.27), residues: 385 loop : -0.68 (0.27), residues: 608 =============================================================================== Job complete usr+sys time: 3335.84 seconds wall clock time: 61 minutes 21.86 seconds (3681.86 seconds total)