Starting phenix.real_space_refine on Sun Mar 10 15:42:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzc_35088/03_2024/8hzc_35088.pdb" } resolution = 3.2 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: 3 Type Number sf(0) Gaussians C 1938 2.51 5 N 546 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "F" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "B" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "C" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.66 Number of scatterers: 3108 At special positions: 0 Unit cell: (103.75, 112.05, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 624 8.00 N 546 7.00 C 1938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 586.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 15 through 24 removed outlier: 6.359A pdb=" N VAL A 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA E 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS E 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU A 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS E 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 49 removed outlier: 5.594A pdb=" N GLU A 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL D 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU E 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.520A pdb=" N GLN A 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN D 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.912A pdb=" N VAL A 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR A 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY D 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN D 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N THR E 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL A 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL E 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA E 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92 removed outlier: 6.839A pdb=" N ILE D 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 98 removed outlier: 6.433A pdb=" N LYS A 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 24 removed outlier: 6.359A pdb=" N VAL F 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA C 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA F 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS C 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU F 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS C 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR F 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 5.595A pdb=" N GLU F 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL B 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL F 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU C 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY F 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.520A pdb=" N GLN F 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN B 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR F 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 82 removed outlier: 6.911A pdb=" N VAL F 70 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL F 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA F 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR C 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL F 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL C 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY F 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA C 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR F 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA C 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N VAL F 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N LYS C 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLN F 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL C 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR F 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.839A pdb=" N ILE B 88 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE F 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 98 removed outlier: 6.432A pdb=" N LYS F 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.67 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 552 1.29 - 1.35: 486 1.35 - 1.42: 102 1.42 - 1.48: 504 1.48 - 1.54: 1470 Bond restraints: 3114 Sorted by residual: bond pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.88e-01 bond pdb=" CA GLY C 86 " pdb=" C GLY C 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 6.69e-01 bond pdb=" CA GLY F 86 " pdb=" C GLY F 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 6.38e-01 bond pdb=" CA GLY D 86 " pdb=" C GLY D 86 " ideal model delta sigma weight residual 1.520 1.515 0.006 7.30e-03 1.88e+04 5.82e-01 bond pdb=" CA GLY E 86 " pdb=" C GLY E 86 " ideal model delta sigma weight residual 1.520 1.515 0.005 7.30e-03 1.88e+04 4.87e-01 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.09: 1294 111.09 - 116.11: 920 116.11 - 121.12: 1012 121.12 - 126.13: 962 126.13 - 131.14: 6 Bond angle restraints: 4194 Sorted by residual: angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 110.71 114.29 -3.58 1.53e+00 4.27e-01 5.48e+00 angle pdb=" N GLY C 86 " pdb=" CA GLY C 86 " pdb=" C GLY C 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.44e+00 angle pdb=" N GLY E 86 " pdb=" CA GLY E 86 " pdb=" C GLY E 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.44e+00 angle pdb=" N GLY F 86 " pdb=" CA GLY F 86 " pdb=" C GLY F 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.43e+00 angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 110.71 114.25 -3.54 1.53e+00 4.27e-01 5.37e+00 ... (remaining 4189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 1620 14.55 - 29.11: 174 29.11 - 43.66: 18 43.66 - 58.21: 18 58.21 - 72.76: 6 Dihedral angle restraints: 1836 sinusoidal: 624 harmonic: 1212 Sorted by residual: dihedral pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY C 41 " pdb=" C GLY C 41 " pdb=" N SER C 42 " pdb=" CA SER C 42 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 251 0.025 - 0.050: 144 0.050 - 0.075: 49 0.075 - 0.099: 29 0.099 - 0.124: 73 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 543 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 43 " -0.004 2.00e-02 2.50e+03 7.94e-03 6.31e-01 pdb=" C LYS C 43 " 0.014 2.00e-02 2.50e+03 pdb=" O LYS C 43 " -0.005 2.00e-02 2.50e+03 pdb=" N THR C 44 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.004 2.00e-02 2.50e+03 7.88e-03 6.21e-01 pdb=" C LYS F 43 " 0.014 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.005 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 43 " 0.004 2.00e-02 2.50e+03 7.87e-03 6.19e-01 pdb=" C LYS E 43 " -0.014 2.00e-02 2.50e+03 pdb=" O LYS E 43 " 0.005 2.00e-02 2.50e+03 pdb=" N THR E 44 " 0.005 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1478 2.98 - 3.46: 2679 3.46 - 3.94: 4531 3.94 - 4.42: 4759 4.42 - 4.90: 9838 Nonbonded interactions: 23285 Sorted by model distance: nonbonded pdb=" O THR F 59 " pdb=" OG1 THR F 59 " model vdw 2.497 2.440 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.497 2.440 nonbonded pdb=" O THR D 59 " pdb=" OG1 THR D 59 " model vdw 2.498 2.440 nonbonded pdb=" O THR A 59 " pdb=" OG1 THR A 59 " model vdw 2.498 2.440 nonbonded pdb=" O THR B 59 " pdb=" OG1 THR B 59 " model vdw 2.498 2.440 ... (remaining 23280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.002 0.015 3114 Z= 0.139 Angle : 0.509 3.582 4194 Z= 0.316 Chirality : 0.052 0.124 546 Planarity : 0.002 0.008 522 Dihedral : 13.527 72.763 1068 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -5.03 (0.27), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.20), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.006 0.002 PHE A 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.338 Fit side-chains REVERT: A 94 PHE cc_start: 0.6187 (t80) cc_final: 0.5657 (t80) REVERT: F 94 PHE cc_start: 0.6098 (t80) cc_final: 0.5564 (t80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2362 time to fit residues: 13.8832 Evaluate side-chains 44 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3114 Z= 0.248 Angle : 0.475 4.196 4194 Z= 0.278 Chirality : 0.051 0.127 546 Planarity : 0.002 0.008 522 Dihedral : 5.191 24.137 444 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.60 % Allowed : 8.97 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.29), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.22), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE D 94 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.358 Fit side-chains REVERT: F 94 PHE cc_start: 0.6080 (t80) cc_final: 0.5636 (t80) REVERT: C 94 PHE cc_start: 0.5604 (t80) cc_final: 0.4813 (t80) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.2336 time to fit residues: 11.9075 Evaluate side-chains 44 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.0370 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 overall best weight: 2.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3114 Z= 0.226 Angle : 0.448 3.840 4194 Z= 0.263 Chirality : 0.050 0.125 546 Planarity : 0.002 0.008 522 Dihedral : 4.950 22.571 444 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.88 % Allowed : 9.29 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 50 PHE 0.009 0.002 PHE F 94 TYR 0.008 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.307 Fit side-chains REVERT: A 94 PHE cc_start: 0.6007 (t80) cc_final: 0.5295 (t80) REVERT: F 94 PHE cc_start: 0.5920 (t80) cc_final: 0.5412 (t80) REVERT: C 94 PHE cc_start: 0.5199 (t80) cc_final: 0.4218 (t80) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.2031 time to fit residues: 11.9006 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 56.6332 > 50: distance: 34 - 148: 22.614 distance: 138 - 139: 3.068 distance: 139 - 140: 3.711 distance: 139 - 142: 5.159 distance: 140 - 141: 5.809 distance: 140 - 145: 5.557 distance: 142 - 143: 9.377 distance: 142 - 144: 8.790 distance: 145 - 146: 4.980 distance: 146 - 147: 8.732 distance: 146 - 149: 15.050 distance: 147 - 148: 13.547 distance: 147 - 152: 4.211 distance: 149 - 150: 15.880 distance: 149 - 151: 13.963 distance: 152 - 153: 3.348 distance: 153 - 154: 5.958 distance: 153 - 156: 5.263 distance: 154 - 155: 6.575 distance: 157 - 158: 3.666 distance: 158 - 161: 3.169 distance: 159 - 160: 8.656 distance: 159 - 164: 10.140 distance: 161 - 163: 14.795 distance: 164 - 165: 3.560 distance: 165 - 166: 4.872 distance: 165 - 168: 8.537 distance: 166 - 169: 10.503 distance: 169 - 170: 4.306 distance: 170 - 171: 5.295 distance: 170 - 173: 3.839 distance: 171 - 172: 9.020 distance: 173 - 174: 4.228 distance: 174 - 175: 11.191 distance: 175 - 176: 8.095 distance: 175 - 177: 11.443 distance: 178 - 179: 5.279 distance: 179 - 180: 4.990 distance: 179 - 182: 6.496 distance: 180 - 181: 4.472 distance: 180 - 187: 7.451 distance: 182 - 183: 7.892 distance: 183 - 184: 8.041 distance: 184 - 185: 9.205 distance: 185 - 186: 7.240 distance: 188 - 189: 8.880 distance: 188 - 191: 5.327 distance: 189 - 190: 11.873 distance: 189 - 194: 9.503 distance: 191 - 192: 9.975 distance: 191 - 193: 6.681 distance: 194 - 195: 6.859 distance: 195 - 196: 3.731 distance: 195 - 198: 8.984 distance: 196 - 197: 19.637 distance: 196 - 201: 18.710 distance: 198 - 199: 15.684 distance: 198 - 200: 28.474 distance: 201 - 202: 13.246 distance: 202 - 203: 12.777 distance: 202 - 205: 4.704 distance: 203 - 204: 12.317 distance: 203 - 210: 9.539 distance: 205 - 206: 21.841 distance: 206 - 207: 16.495 distance: 207 - 208: 32.453 distance: 207 - 209: 32.451