Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 08:53:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/08_2023/7nk9_12434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/08_2023/7nk9_12434.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/7nk9_12434/08_2023/7nk9_12434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/08_2023/7nk9_12434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/08_2023/7nk9_12434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/08_2023/7nk9_12434.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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 5873 2.51 5 N 1460 2.21 5 O 1560 1.98 5 H 9158 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 227": "OD1" <-> "OD2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 32": "OD1" <-> "OD2" Residue "a PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 177": "OE1" <-> "OE2" Residue "d ASP 53": "OD1" <-> "OD2" 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: 18081 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 446 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 3, 'TRANS': 26} Chain breaks: 1 Chain: "H" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1239 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 3 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 957 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "d" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 920 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Time building chain proxies: 7.53, per 1000 atoms: 0.42 Number of scatterers: 18081 At special positions: 0 Unit cell: (97.94, 79.68, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1560 8.00 N 1460 7.00 C 5873 6.00 H 9158 1.00 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: 15.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 4 sheets defined 82.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.514A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 117 Processing helix chain 'L' and resid 4 through 46 Processing helix chain 'L' and resid 49 through 80 removed outlier: 3.681A pdb=" N PHE L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.954A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 81 removed outlier: 4.627A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.631A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.697A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 3.732A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.805A pdb=" N ALA N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.748A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 81 removed outlier: 4.134A pdb=" N PHE O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.518A pdb=" N ALA O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR O 68 " --> pdb=" O VAL O 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.568A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 4.259A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.630A pdb=" N ALA P 66 " --> pdb=" O GLY P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.615A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.976A pdb=" N PHE Q 54 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.701A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.846A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.029A pdb=" N ALA R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.586A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 80 removed outlier: 4.761A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.832A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.635A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.197A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.972A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU T 77 " --> pdb=" O ALA T 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 53 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.690A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.606A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.648A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 205 Proline residue: a 182 - end of helix removed outlier: 3.737A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.712A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.953A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.660A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 82 removed outlier: 3.515A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 59 Processing sheet with id=AA1, first strand: chain 'G' and resid 223 through 224 removed outlier: 6.291A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.862A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'a' and resid 112 through 114 817 hydrogen bonds defined for protein. 2430 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: 7.24 Time building geometry restraints manager: 16.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9157 1.03 - 1.23: 5 1.23 - 1.42: 3696 1.42 - 1.61: 5342 1.61 - 1.81: 59 Bond restraints: 18259 Sorted by residual: bond pdb=" CG GLN a 76 " pdb=" CD GLN a 76 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CG1 ILE O 9 " pdb=" CD1 ILE O 9 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.01e-01 bond pdb=" CA VAL H 23 " pdb=" C VAL H 23 " ideal model delta sigma weight residual 1.527 1.520 0.007 8.50e-03 1.38e+04 7.00e-01 bond pdb=" CB THR P 10 " pdb=" CG2 THR P 10 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.73e-01 bond pdb=" CB MET L 21 " pdb=" CG MET L 21 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.40e-01 ... (remaining 18254 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.92: 321 106.92 - 113.68: 21750 113.68 - 120.44: 6388 120.44 - 127.20: 4582 127.20 - 133.95: 81 Bond angle restraints: 33122 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 121.14 116.27 4.87 1.75e+00 3.27e-01 7.74e+00 angle pdb=" CA PRO G 226 " pdb=" C PRO G 226 " pdb=" N ASP G 227 " ideal model delta sigma weight residual 115.12 118.30 -3.18 1.25e+00 6.40e-01 6.49e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.47e+00 angle pdb=" N GLN a 76 " pdb=" CA GLN a 76 " pdb=" CB GLN a 76 " ideal model delta sigma weight residual 110.12 113.73 -3.61 1.47e+00 4.63e-01 6.03e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.40 114.08 -3.68 1.63e+00 3.76e-01 5.10e+00 ... (remaining 33117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 6398 16.94 - 33.87: 601 33.87 - 50.81: 60 50.81 - 67.75: 10 67.75 - 84.68: 6 Dihedral angle restraints: 7075 sinusoidal: 3123 harmonic: 3952 Sorted by residual: dihedral pdb=" CA GLU G 225 " pdb=" C GLU G 225 " pdb=" N PRO G 226 " pdb=" CA PRO G 226 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE P 58 " pdb=" C PHE P 58 " pdb=" N ILE P 59 " pdb=" CA ILE P 59 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA ARG M 45 " pdb=" CB ARG M 45 " pdb=" CG ARG M 45 " pdb=" CD ARG M 45 " ideal model delta sinusoidal sigma weight residual -180.00 -126.04 -53.96 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 7072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 929 0.029 - 0.059: 305 0.059 - 0.088: 180 0.088 - 0.118: 39 0.118 - 0.147: 7 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CA PRO H 36 " pdb=" N PRO H 36 " pdb=" C PRO H 36 " pdb=" CB PRO H 36 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE H 63 " pdb=" N ILE H 63 " pdb=" C ILE H 63 " pdb=" CB ILE H 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA TYR a 145 " pdb=" N TYR a 145 " pdb=" C TYR a 145 " pdb=" CB TYR a 145 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1457 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C PHE a 99 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C PHE a 97 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE a 97 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL a 98 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR a 95 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C THR a 95 " -0.031 2.00e-02 2.50e+03 pdb=" O THR a 95 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE a 96 " 0.010 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1681 2.23 - 2.82: 41110 2.82 - 3.42: 52733 3.42 - 4.01: 70737 4.01 - 4.60: 109853 Nonbonded interactions: 276114 Sorted by model distance: nonbonded pdb=" O LEU G 57 " pdb=" HG SER G 61 " model vdw 1.639 1.850 nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.651 1.850 nonbonded pdb=" H THR H 21 " pdb=" O GLU H 54 " model vdw 1.657 1.850 nonbonded pdb=" OE1 GLN R 46 " pdb="HH22 ARG R 52 " model vdw 1.660 1.850 nonbonded pdb=" HE ARG H 37 " pdb=" OE2 GLU T 48 " model vdw 1.666 1.850 ... (remaining 276109 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 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'O' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'P' selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 8.600 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: 0.290 Extract box with map and model: 26.180 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 58.960 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.003 0.033 9101 Z= 0.228 Angle : 0.495 5.183 12360 Z= 0.277 Chirality : 0.039 0.147 1460 Planarity : 0.005 0.043 1587 Dihedral : 13.032 84.683 3095 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 1.61 (0.26), residues: 1189 helix: 1.21 (0.18), residues: 950 sheet: -1.10 (0.85), residues: 34 loop : 1.28 (0.49), residues: 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 119 average time/residue: 2.7330 time to fit residues: 348.2420 Evaluate side-chains 78 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.6059 time to fit residues: 3.4700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 90 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 71 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9101 Z= 0.233 Angle : 0.523 5.443 12360 Z= 0.280 Chirality : 0.040 0.151 1460 Planarity : 0.005 0.075 1587 Dihedral : 3.788 19.984 1261 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 1.51 % 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: 2.86 (0.25), residues: 1189 helix: 2.08 (0.17), residues: 964 sheet: -1.13 (0.86), residues: 34 loop : 1.80 (0.50), residues: 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 2.2416 time to fit residues: 224.0018 Evaluate side-chains 79 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.5363 time to fit residues: 3.3418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 0.0040 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9101 Z= 0.239 Angle : 0.511 5.546 12360 Z= 0.270 Chirality : 0.039 0.155 1460 Planarity : 0.004 0.043 1587 Dihedral : 3.779 18.552 1261 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.86 % 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: 3.61 (0.24), residues: 1189 helix: 2.80 (0.17), residues: 921 sheet: -1.22 (0.85), residues: 34 loop : 1.34 (0.43), residues: 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 2.2253 time to fit residues: 208.0607 Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.7746 time to fit residues: 9.2850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9101 Z= 0.280 Angle : 0.521 5.483 12360 Z= 0.276 Chirality : 0.040 0.163 1460 Planarity : 0.004 0.046 1587 Dihedral : 3.837 17.722 1261 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.97 % 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: 3.70 (0.24), residues: 1189 helix: 2.90 (0.16), residues: 922 sheet: -1.31 (0.83), residues: 34 loop : 1.23 (0.42), residues: 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 2.1535 time to fit residues: 201.9295 Evaluate side-chains 85 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 1.6570 time to fit residues: 7.0215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 9101 Z= 0.304 Angle : 0.532 5.544 12360 Z= 0.284 Chirality : 0.040 0.165 1460 Planarity : 0.004 0.047 1587 Dihedral : 3.937 29.398 1261 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.21 % 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: 3.72 (0.24), residues: 1189 helix: 2.93 (0.16), residues: 921 sheet: -1.28 (0.85), residues: 34 loop : 1.18 (0.42), residues: 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 2.1837 time to fit residues: 209.8148 Evaluate side-chains 82 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.8316 time to fit residues: 9.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9101 Z= 0.214 Angle : 0.509 9.362 12360 Z= 0.265 Chirality : 0.039 0.147 1460 Planarity : 0.004 0.043 1587 Dihedral : 3.824 22.531 1261 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 1.16 % 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: 3.91 (0.24), residues: 1189 helix: 3.05 (0.16), residues: 924 sheet: -1.18 (0.86), residues: 34 loop : 1.27 (0.43), residues: 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 2.2557 time to fit residues: 218.1251 Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.5520 time to fit residues: 3.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9101 Z= 0.292 Angle : 0.533 7.426 12360 Z= 0.282 Chirality : 0.040 0.166 1460 Planarity : 0.004 0.047 1587 Dihedral : 3.866 22.032 1261 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 1.74 % 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: 3.81 (0.24), residues: 1189 helix: 2.98 (0.16), residues: 924 sheet: -1.27 (0.85), residues: 34 loop : 1.21 (0.43), residues: 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 83 average time/residue: 2.4309 time to fit residues: 219.0280 Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.9018 time to fit residues: 7.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9101 Z= 0.227 Angle : 0.514 7.327 12360 Z= 0.268 Chirality : 0.039 0.150 1460 Planarity : 0.004 0.044 1587 Dihedral : 3.804 20.693 1261 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 1.39 % 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: 3.92 (0.24), residues: 1189 helix: 3.05 (0.16), residues: 924 sheet: -1.18 (0.86), residues: 34 loop : 1.27 (0.43), residues: 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 2.2409 time to fit residues: 202.8079 Evaluate side-chains 83 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.9325 time to fit residues: 3.7786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 67 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: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9101 Z= 0.261 Angle : 0.529 6.710 12360 Z= 0.277 Chirality : 0.040 0.159 1460 Planarity : 0.004 0.048 1587 Dihedral : 3.826 20.775 1261 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.28 % 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: 3.88 (0.24), residues: 1189 helix: 3.04 (0.16), residues: 924 sheet: -1.25 (0.86), residues: 34 loop : 1.19 (0.42), residues: 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 2.1599 time to fit residues: 200.2476 Evaluate side-chains 79 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.9889 time to fit residues: 3.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9101 Z= 0.245 Angle : 0.524 6.337 12360 Z= 0.274 Chirality : 0.040 0.155 1460 Planarity : 0.004 0.099 1587 Dihedral : 3.831 21.150 1261 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 1.05 % 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: 3.90 (0.24), residues: 1189 helix: 3.06 (0.16), residues: 924 sheet: -1.20 (0.87), residues: 34 loop : 1.18 (0.42), residues: 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 2.2423 time to fit residues: 198.2678 Evaluate side-chains 80 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.9799 time to fit residues: 3.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063646 restraints weight = 59855.801| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.15 r_work: 0.2890 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9101 Z= 0.228 Angle : 0.522 6.865 12360 Z= 0.271 Chirality : 0.039 0.152 1460 Planarity : 0.004 0.058 1587 Dihedral : 3.782 20.945 1261 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.51 % 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: 3.96 (0.24), residues: 1189 helix: 3.10 (0.16), residues: 924 sheet: -1.16 (0.87), residues: 34 loop : 1.17 (0.42), residues: 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5490.61 seconds wall clock time: 97 minutes 23.89 seconds (5843.89 seconds total)