Starting phenix.real_space_refine on Sun Mar 17 14:05:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/03_2024/7nk9_12434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/03_2024/7nk9_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_12434/03_2024/7nk9_12434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/03_2024/7nk9_12434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/03_2024/7nk9_12434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk9_12434/03_2024/7nk9_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-dev-5265/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: 8.03, per 1000 atoms: 0.44 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: 15.21 Conformation dependent library (CDL) restraints added in 1.8 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: 0.88 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: 6.68 Time building geometry restraints manager: 15.72 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: 7446 16.94 - 33.87: 658 33.87 - 50.81: 217 50.81 - 67.75: 206 67.75 - 84.68: 6 Dihedral angle restraints: 8533 sinusoidal: 4581 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 8530 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: 11.580 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: 0.270 Extract box with map and model: 25.500 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 57.870 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.750 ------------------------------------------------------------------------------- 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 % Allowed : 0.12 % Favored : 99.88 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.001 PHE P 69 TYR 0.010 0.001 TYR a 145 ARG 0.003 0.000 ARG P 45 *********************** 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 : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 47 PRO cc_start: 0.8191 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: b 66 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8181 (tmmm) REVERT: d 33 GLN cc_start: 0.8232 (tp40) cc_final: 0.7868 (tp40) outliers start: 0 outliers final: 1 residues processed: 119 average time/residue: 2.6761 time to fit residues: 341.2210 Evaluate side-chains 79 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 57 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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: 0.8523 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9101 Z= 0.270 Angle : 0.527 5.496 12360 Z= 0.285 Chirality : 0.040 0.157 1460 Planarity : 0.005 0.072 1587 Dihedral : 3.956 25.012 1264 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.39 % Allowed : 7.90 % Favored : 90.71 % 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: 2.80 (0.25), residues: 1189 helix: 2.05 (0.17), residues: 961 sheet: -1.17 (0.85), residues: 34 loop : 1.74 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.017 0.002 PHE M 74 TYR 0.029 0.001 TYR a 145 ARG 0.007 0.001 ARG P 45 *********************** 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: 12 poor density : 85 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 61 LEU cc_start: 0.8155 (mp) cc_final: 0.7839 (mp) REVERT: S 65 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: b 46 SER cc_start: 0.9062 (m) cc_final: 0.8772 (m) REVERT: b 66 LYS cc_start: 0.8426 (tmmt) cc_final: 0.8136 (tmmm) REVERT: d 33 GLN cc_start: 0.8290 (tp40) cc_final: 0.7946 (tp40) outliers start: 12 outliers final: 3 residues processed: 92 average time/residue: 2.3603 time to fit residues: 234.9890 Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 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: 0.6782 ------------------------------------------------------------------------------- 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: 0.1462 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= 0.234 Angle : 0.505 5.381 12360 Z= 0.268 Chirality : 0.040 0.152 1460 Planarity : 0.004 0.045 1587 Dihedral : 3.803 19.130 1261 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.74 % Allowed : 9.76 % Favored : 88.50 % 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: 3.58 (0.24), residues: 1189 helix: 2.77 (0.16), residues: 921 sheet: -1.11 (0.87), residues: 34 loop : 1.35 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.001 PHE M 74 TYR 0.025 0.001 TYR a 145 ARG 0.006 0.001 ARG P 45 *********************** 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 96 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: S 65 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: b 46 SER cc_start: 0.9042 (m) cc_final: 0.8826 (m) REVERT: b 66 LYS cc_start: 0.8419 (tmmt) cc_final: 0.8136 (tmmm) REVERT: d 33 GLN cc_start: 0.8294 (tp40) cc_final: 0.7962 (tp40) outliers start: 15 outliers final: 6 residues processed: 87 average time/residue: 2.2476 time to fit residues: 212.3319 Evaluate side-chains 83 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8534 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9101 Z= 0.260 Angle : 0.509 5.430 12360 Z= 0.270 Chirality : 0.039 0.159 1460 Planarity : 0.004 0.046 1587 Dihedral : 3.820 18.045 1261 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.97 % Allowed : 10.69 % Favored : 87.34 % 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: 3.75 (0.24), residues: 1189 helix: 2.92 (0.16), residues: 922 sheet: -1.21 (0.85), residues: 34 loop : 1.28 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE M 74 TYR 0.023 0.001 TYR a 145 ARG 0.005 0.000 ARG b 72 *********************** 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 95 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 61 LEU cc_start: 0.8135 (mp) cc_final: 0.7865 (mt) REVERT: M 75 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8030 (tmm) REVERT: P 21 MET cc_start: 0.8434 (mmm) cc_final: 0.8141 (mmp) REVERT: S 65 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: a 247 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8043 (mp) REVERT: b 66 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8168 (tmmm) REVERT: d 33 GLN cc_start: 0.8386 (tp40) cc_final: 0.8061 (tp40) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 2.2560 time to fit residues: 212.9231 Evaluate side-chains 87 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 46 GLU 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: 0.9980 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.1761 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= 0.307 Angle : 0.522 5.487 12360 Z= 0.280 Chirality : 0.040 0.166 1460 Planarity : 0.004 0.048 1587 Dihedral : 3.879 17.601 1261 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.67 % Allowed : 11.27 % Favored : 86.06 % 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: 3.77 (0.24), residues: 1189 helix: 2.95 (0.16), residues: 921 sheet: -1.24 (0.83), residues: 34 loop : 1.25 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.016 0.002 PHE M 74 TYR 0.022 0.001 TYR a 145 ARG 0.005 0.000 ARG b 72 *********************** 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 98 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8439 (t) REVERT: M 75 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7987 (tmm) REVERT: P 48 GLU cc_start: 0.7439 (pm20) cc_final: 0.7009 (pp20) REVERT: S 65 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: a 247 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8100 (mp) REVERT: b 66 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8181 (tmmm) REVERT: d 33 GLN cc_start: 0.8430 (tp40) cc_final: 0.8110 (tp40) outliers start: 23 outliers final: 11 residues processed: 88 average time/residue: 2.2141 time to fit residues: 212.8040 Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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: 0.8530 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9101 Z= 0.220 Angle : 0.498 5.358 12360 Z= 0.263 Chirality : 0.039 0.149 1460 Planarity : 0.004 0.045 1587 Dihedral : 3.825 18.118 1261 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.09 % Allowed : 12.54 % Favored : 85.37 % 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: 3.03 (0.16), residues: 924 sheet: -1.23 (0.85), residues: 34 loop : 1.33 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE M 74 TYR 0.020 0.001 TYR a 145 ARG 0.006 0.000 ARG b 72 *********************** 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 99 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (t) REVERT: M 75 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: N 65 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: a 247 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (mp) REVERT: b 66 LYS cc_start: 0.8464 (tmmt) cc_final: 0.8182 (tmmm) REVERT: d 33 GLN cc_start: 0.8415 (tp40) cc_final: 0.8096 (tp40) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 2.2510 time to fit residues: 227.2511 Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8953 > 50: distance: 203 - 255: 11.533 distance: 219 - 274: 12.465 distance: 233 - 284: 21.826 distance: 247 - 255: 15.119 distance: 248 - 304: 14.177 distance: 255 - 256: 15.478 distance: 255 - 263: 24.307 distance: 256 - 257: 5.967 distance: 256 - 259: 18.845 distance: 256 - 264: 23.890 distance: 257 - 258: 15.268 distance: 257 - 274: 5.135 distance: 258 - 321: 16.176 distance: 259 - 260: 5.276 distance: 259 - 265: 7.132 distance: 259 - 266: 15.892 distance: 260 - 261: 24.774 distance: 260 - 262: 34.120 distance: 260 - 267: 7.550 distance: 261 - 268: 19.668 distance: 261 - 269: 11.016 distance: 261 - 270: 25.465 distance: 262 - 271: 18.475 distance: 262 - 272: 11.414 distance: 262 - 273: 12.915 distance: 274 - 275: 27.710 distance: 274 - 279: 19.802 distance: 275 - 276: 19.201 distance: 275 - 278: 42.026 distance: 275 - 280: 13.268 distance: 276 - 277: 31.268 distance: 276 - 284: 16.228 distance: 278 - 283: 7.619 distance: 284 - 285: 14.354 distance: 284 - 295: 22.083 distance: 285 - 286: 12.293 distance: 285 - 288: 19.965 distance: 285 - 296: 7.993 distance: 286 - 287: 15.983 distance: 286 - 304: 6.520 distance: 287 - 350: 10.540 distance: 288 - 289: 14.338 distance: 288 - 297: 13.889 distance: 288 - 298: 12.031 distance: 289 - 291: 13.338 distance: 290 - 292: 5.258 distance: 290 - 299: 7.561 distance: 291 - 293: 9.754 distance: 291 - 300: 9.964 distance: 292 - 294: 4.836 distance: 292 - 301: 12.345 distance: 293 - 294: 4.211 distance: 293 - 302: 7.799 distance: 294 - 303: 3.306 distance: 304 - 305: 17.028 distance: 304 - 312: 5.211 distance: 305 - 306: 26.033 distance: 305 - 308: 25.866 distance: 305 - 313: 29.023 distance: 306 - 321: 33.225 distance: 307 - 370: 36.911 distance: 308 - 309: 14.512 distance: 308 - 314: 31.177 distance: 308 - 315: 7.202 distance: 309 - 310: 28.505 distance: 309 - 316: 12.160 distance: 309 - 317: 35.890 distance: 310 - 311: 23.468 distance: 311 - 318: 20.790 distance: 311 - 319: 7.718 distance: 311 - 320: 21.424 distance: 321 - 322: 43.280 distance: 321 - 326: 35.056 distance: 322 - 323: 19.818 distance: 322 - 325: 22.481 distance: 322 - 327: 6.908 distance: 323 - 324: 19.612 distance: 323 - 331: 10.999 distance: 324 - 386: 19.333 distance: 325 - 328: 20.020 distance: 325 - 329: 7.805 distance: 325 - 330: 37.224 distance: 331 - 332: 16.948 distance: 331 - 339: 11.547 distance: 332 - 333: 11.955 distance: 332 - 335: 20.485 distance: 332 - 340: 31.912 distance: 333 - 334: 32.371 distance: 333 - 350: 21.722 distance: 334 - 406: 20.993 distance: 335 - 336: 14.319 distance: 335 - 341: 8.952 distance: 335 - 342: 12.889 distance: 336 - 337: 21.818 distance: 336 - 338: 24.048 distance: 336 - 343: 12.968 distance: 337 - 344: 23.462 distance: 337 - 345: 12.428 distance: 337 - 346: 24.494 distance: 338 - 347: 5.091 distance: 338 - 348: 19.168 distance: 338 - 349: 8.744 distance: 350 - 351: 27.572 distance: 350 - 361: 37.720 distance: 351 - 352: 36.653 distance: 351 - 354: 15.242 distance: 351 - 362: 14.716 distance: 352 - 353: 9.894 distance: 352 - 370: 34.421 distance: 354 - 355: 11.013 distance: 354 - 363: 6.801 distance: 354 - 364: 13.141 distance: 355 - 356: 24.687 distance: 355 - 357: 8.844 distance: 356 - 358: 15.135 distance: 356 - 365: 11.255 distance: 357 - 359: 14.648 distance: 357 - 366: 10.762 distance: 358 - 360: 13.494 distance: 358 - 367: 22.092 distance: 359 - 360: 14.757 distance: 359 - 368: 8.086 distance: 360 - 369: 8.307 distance: 370 - 371: 4.810 distance: 370 - 377: 22.488 distance: 371 - 372: 37.849 distance: 371 - 374: 23.391 distance: 371 - 378: 13.201 distance: 372 - 373: 9.110 distance: 372 - 386: 50.904 distance: 374 - 375: 8.041 distance: 374 - 376: 33.884 distance: 374 - 379: 11.447 distance: 375 - 380: 25.769 distance: 375 - 381: 21.929 distance: 375 - 382: 7.499 distance: 376 - 383: 14.603 distance: 376 - 384: 16.642 distance: 386 - 387: 22.952 distance: 386 - 397: 9.184 distance: 387 - 388: 33.427 distance: 387 - 390: 38.113 distance: 387 - 398: 15.176 distance: 388 - 389: 23.955 distance: 388 - 406: 21.124 distance: 390 - 391: 21.170 distance: 390 - 399: 17.031 distance: 390 - 400: 32.518 distance: 391 - 392: 20.544 distance: 391 - 393: 17.598 distance: 392 - 394: 10.352 distance: 392 - 401: 5.641 distance: 393 - 395: 13.432 distance: 393 - 402: 10.164 distance: 394 - 396: 12.171 distance: 394 - 403: 7.387 distance: 395 - 396: 14.873 distance: 395 - 404: 18.237 distance: 396 - 405: 13.514 distance: 406 - 407: 42.030 distance: 406 - 411: 30.416 distance: 407 - 408: 16.598 distance: 407 - 410: 27.158 distance: 407 - 412: 31.015 distance: 408 - 409: 8.870 distance: 408 - 416: 26.443 distance: 410 - 413: 6.259 distance: 410 - 415: 16.300