Starting phenix.real_space_refine on Sat Aug 3 06:30:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/08_2024/6vcc_21148.cif" } resolution = 3.6 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= 0.011 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4896 2.51 5 N 1236 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "C" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "D" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "I" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "J" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "L" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Time building chain proxies: 4.65, per 1000 atoms: 0.61 Number of scatterers: 7572 At special positions: 0 Unit cell: (90, 92, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1416 8.00 N 1236 7.00 C 4896 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 15.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.620A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.655A pdb=" N GLY A 83 " --> pdb=" O CYS A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.636A pdb=" N PHE B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.765A pdb=" N GLY B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.750A pdb=" N PHE C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.609A pdb=" N GLY C 83 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.663A pdb=" N PHE D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.757A pdb=" N PHE E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 46 removed outlier: 3.587A pdb=" N PHE F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.598A pdb=" N GLY F 83 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.867A pdb=" N VAL G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.800A pdb=" N GLY G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.946A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU H 47 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.529A pdb=" N GLY H 83 " --> pdb=" O CYS H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.575A pdb=" N GLY I 83 " --> pdb=" O CYS I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.921A pdb=" N VAL J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLY J 83 " --> pdb=" O CYS J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 45 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.559A pdb=" N GLY K 83 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.895A pdb=" N VAL L 46 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L 47 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 5.164A pdb=" N VAL A 86 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER A 87 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 17 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 89 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 28 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 6.963A pdb=" N LEU B 28 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.940A pdb=" N LEU C 28 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL D 86 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER D 87 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 17 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 18 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 28 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 86 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 87 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 17 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 18 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 28 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F 86 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER F 87 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE F 17 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.543A pdb=" N THR G 14 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 29 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.586A pdb=" N LYS H 30 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.794A pdb=" N ILE H 17 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU H 89 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL H 86 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS I 30 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 18 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR I 14 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER I 87 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 17 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU I 89 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 86 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS J 30 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 17 through 18 removed outlier: 6.863A pdb=" N ILE J 17 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU J 89 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL J 86 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS K 30 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR K 18 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR K 14 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER K 87 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE K 17 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU K 89 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL K 86 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 30 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 14 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 18 removed outlier: 6.658A pdb=" N ILE L 17 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU L 89 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL L 86 " --> pdb=" O LYS L 58 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 489 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: 1.72 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2431 1.34 - 1.46: 1687 1.46 - 1.58: 3598 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7752 Sorted by residual: bond pdb=" N LYS L 54 " pdb=" CA LYS L 54 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.23e-02 6.61e+03 3.96e+00 bond pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.06e+00 bond pdb=" C VAL A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.73e+00 bond pdb=" C VAL B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.51e+00 bond pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.70e-02 3.46e+03 1.24e+00 ... (remaining 7747 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 320 107.28 - 113.95: 4183 113.95 - 120.63: 3075 120.63 - 127.30: 2853 127.30 - 133.98: 69 Bond angle restraints: 10500 Sorted by residual: angle pdb=" C LEU F 47 " pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 122.46 127.44 -4.98 1.41e+00 5.03e-01 1.25e+01 angle pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " pdb=" CG GLN F 48 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.50e+00 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 106.55 110.06 -3.51 1.45e+00 4.76e-01 5.86e+00 angle pdb=" C LEU H 89 " pdb=" N VAL H 90 " pdb=" CA VAL H 90 " ideal model delta sigma weight residual 121.70 125.73 -4.03 1.80e+00 3.09e-01 5.01e+00 angle pdb=" C LEU J 89 " pdb=" N VAL J 90 " pdb=" CA VAL J 90 " ideal model delta sigma weight residual 121.70 125.70 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4277 17.65 - 35.30: 347 35.30 - 52.95: 47 52.95 - 70.60: 4 70.60 - 88.24: 5 Dihedral angle restraints: 4680 sinusoidal: 1944 harmonic: 2736 Sorted by residual: dihedral pdb=" CB GLU H 24 " pdb=" CG GLU H 24 " pdb=" CD GLU H 24 " pdb=" OE1 GLU H 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.24 -88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU I 24 " pdb=" CG GLU I 24 " pdb=" CD GLU I 24 " pdb=" OE1 GLU I 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.11 -88.11 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ASP D 61 " pdb=" CB ASP D 61 " pdb=" CG ASP D 61 " pdb=" OD1 ASP D 61 " ideal model delta sinusoidal sigma weight residual -30.00 -80.47 50.47 1 2.00e+01 2.50e-03 8.72e+00 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 684 0.039 - 0.078: 292 0.078 - 0.118: 135 0.118 - 0.157: 31 0.157 - 0.196: 10 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CB ILE F 38 " pdb=" CA ILE F 38 " pdb=" CG1 ILE F 38 " pdb=" CG2 ILE F 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CB ILE A 38 " pdb=" CA ILE A 38 " pdb=" CG1 ILE A 38 " pdb=" CG2 ILE A 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE E 38 " pdb=" CA ILE E 38 " pdb=" CG1 ILE E 38 " pdb=" CG2 ILE E 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 1149 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 33 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO C 34 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO H 34 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 77 " 0.108 9.50e-02 1.11e+02 5.00e-02 3.19e+00 pdb=" NE ARG H 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG H 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG H 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 77 " 0.012 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6085 3.31 - 3.84: 12354 3.84 - 4.37: 13207 4.37 - 4.90: 24311 Nonbonded interactions: 57530 Sorted by model distance: nonbonded pdb=" ND2 ASN D 82 " pdb=" OD1 ASP I 63 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP E 63 " pdb=" ND2 ASN J 82 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP D 63 " pdb=" ND2 ASN I 82 " model vdw 2.425 3.120 nonbonded pdb=" ND2 ASN E 82 " pdb=" OD1 ASP J 63 " model vdw 2.433 3.120 nonbonded pdb=" OD1 ASP B 63 " pdb=" ND2 ASN G 82 " model vdw 2.442 3.120 ... (remaining 57525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 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 : 0.004 0.036 7752 Z= 0.236 Angle : 0.664 6.330 10500 Z= 0.376 Chirality : 0.054 0.196 1152 Planarity : 0.006 0.050 1356 Dihedral : 12.504 88.244 2904 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % 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: -4.54 (0.24), residues: 912 helix: -3.99 (0.12), residues: 72 sheet: -3.22 (0.23), residues: 360 loop : -2.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 88 HIS 0.004 0.002 HIS J 19 PHE 0.008 0.001 PHE E 64 TYR 0.015 0.002 TYR D 18 ARG 0.023 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6888 (mmtt) REVERT: B 70 GLU cc_start: 0.7086 (tt0) cc_final: 0.6733 (tt0) REVERT: C 23 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6172 (mt-10) REVERT: D 15 LYS cc_start: 0.7854 (mttt) cc_final: 0.7217 (mmtt) REVERT: D 23 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6174 (mt-10) REVERT: D 54 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7117 (mtpt) REVERT: D 55 TYR cc_start: 0.7498 (m-80) cc_final: 0.7077 (m-80) REVERT: E 54 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6724 (mtmm) REVERT: F 66 VAL cc_start: 0.8090 (m) cc_final: 0.7838 (m) REVERT: H 20 LEU cc_start: 0.8541 (mp) cc_final: 0.8293 (mt) REVERT: H 54 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7695 (mmtm) REVERT: I 72 SER cc_start: 0.7102 (m) cc_final: 0.6847 (p) REVERT: J 60 MET cc_start: 0.8315 (tpp) cc_final: 0.8097 (tpp) REVERT: K 49 ARG cc_start: 0.6228 (mmm160) cc_final: 0.5993 (mmp80) REVERT: K 69 GLU cc_start: 0.6371 (pt0) cc_final: 0.5993 (pt0) REVERT: K 74 ASP cc_start: 0.6733 (m-30) cc_final: 0.6384 (p0) REVERT: L 34 PRO cc_start: 0.6822 (Cg_endo) cc_final: 0.6132 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2544 time to fit residues: 73.2494 Evaluate side-chains 184 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 82 ASN J 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7752 Z= 0.264 Angle : 0.617 8.878 10500 Z= 0.300 Chirality : 0.050 0.148 1152 Planarity : 0.005 0.049 1356 Dihedral : 4.208 12.759 1008 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.69 % Allowed : 13.93 % Favored : 82.38 % 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: -3.85 (0.25), residues: 912 helix: -1.60 (0.38), residues: 72 sheet: -2.97 (0.24), residues: 360 loop : -2.29 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 88 HIS 0.005 0.002 HIS F 19 PHE 0.016 0.002 PHE E 43 TYR 0.016 0.002 TYR A 27 ARG 0.004 0.001 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7219 (mtpp) cc_final: 0.7009 (mmtt) REVERT: B 58 LYS cc_start: 0.8148 (tttt) cc_final: 0.7780 (tttp) REVERT: C 23 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6284 (mt-10) REVERT: D 54 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7049 (mtpt) REVERT: D 70 GLU cc_start: 0.5644 (tt0) cc_final: 0.5152 (tt0) REVERT: H 27 TYR cc_start: 0.8405 (m-80) cc_final: 0.8123 (m-80) REVERT: H 54 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7640 (mmtm) REVERT: K 49 ARG cc_start: 0.6377 (mmm160) cc_final: 0.6107 (mmp80) REVERT: K 74 ASP cc_start: 0.6966 (m-30) cc_final: 0.6701 (t0) outliers start: 31 outliers final: 18 residues processed: 218 average time/residue: 0.2415 time to fit residues: 66.8250 Evaluate side-chains 198 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7752 Z= 0.207 Angle : 0.558 8.550 10500 Z= 0.269 Chirality : 0.049 0.203 1152 Planarity : 0.004 0.045 1356 Dihedral : 4.052 12.333 1008 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.98 % Allowed : 17.14 % Favored : 79.88 % 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: -3.32 (0.26), residues: 912 helix: 0.42 (0.54), residues: 72 sheet: -2.71 (0.24), residues: 360 loop : -2.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 88 HIS 0.004 0.002 HIS D 19 PHE 0.019 0.002 PHE I 64 TYR 0.014 0.001 TYR G 55 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7193 (mtpp) cc_final: 0.6982 (mmtt) REVERT: B 58 LYS cc_start: 0.8125 (tttt) cc_final: 0.7714 (tttp) REVERT: C 23 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6282 (mt-10) REVERT: D 54 LYS cc_start: 0.7557 (mtpp) cc_final: 0.6935 (mtpt) REVERT: D 70 GLU cc_start: 0.5794 (tt0) cc_final: 0.5189 (tt0) REVERT: H 27 TYR cc_start: 0.8437 (m-80) cc_final: 0.8149 (m-80) REVERT: H 54 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7743 (mmtm) REVERT: J 17 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8262 (mt) REVERT: J 30 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7950 (mmtt) REVERT: J 60 MET cc_start: 0.8530 (tpp) cc_final: 0.8244 (tpp) REVERT: K 47 LEU cc_start: 0.8703 (mm) cc_final: 0.8209 (mm) REVERT: K 74 ASP cc_start: 0.6965 (m-30) cc_final: 0.6687 (p0) outliers start: 25 outliers final: 21 residues processed: 197 average time/residue: 0.2417 time to fit residues: 60.6857 Evaluate side-chains 197 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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: 0.7081 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7752 Z= 0.345 Angle : 0.638 9.457 10500 Z= 0.307 Chirality : 0.051 0.147 1152 Planarity : 0.005 0.051 1356 Dihedral : 4.586 15.490 1008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.05 % Allowed : 17.98 % Favored : 77.98 % 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: -3.17 (0.27), residues: 912 helix: 0.53 (0.61), residues: 84 sheet: -2.70 (0.25), residues: 360 loop : -2.02 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 88 HIS 0.005 0.003 HIS F 19 PHE 0.022 0.002 PHE L 64 TYR 0.015 0.002 TYR B 27 ARG 0.003 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8210 (tttt) cc_final: 0.7826 (tttp) REVERT: D 54 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7231 (mtpt) REVERT: D 70 GLU cc_start: 0.5753 (tt0) cc_final: 0.5425 (tt0) REVERT: E 54 LYS cc_start: 0.7673 (mmmt) cc_final: 0.6752 (mptt) REVERT: F 60 MET cc_start: 0.7739 (tpp) cc_final: 0.6638 (tmm) REVERT: F 64 PHE cc_start: 0.8215 (m-80) cc_final: 0.8006 (m-80) REVERT: G 71 ILE cc_start: 0.8070 (mt) cc_final: 0.7832 (mm) REVERT: H 27 TYR cc_start: 0.8479 (m-80) cc_final: 0.8231 (m-80) REVERT: I 30 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7777 (mttt) REVERT: K 54 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8035 (mmmt) REVERT: K 74 ASP cc_start: 0.7023 (m-30) cc_final: 0.6712 (p0) outliers start: 34 outliers final: 26 residues processed: 213 average time/residue: 0.2429 time to fit residues: 65.9754 Evaluate side-chains 215 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 55.9741 > 50: distance: 83 - 89: 25.099 distance: 89 - 90: 11.272 distance: 90 - 91: 36.957 distance: 90 - 93: 13.372 distance: 91 - 92: 16.076 distance: 91 - 95: 27.064 distance: 93 - 94: 28.667 distance: 95 - 96: 16.929 distance: 96 - 97: 17.229 distance: 96 - 99: 14.723 distance: 97 - 98: 9.561 distance: 97 - 103: 14.735 distance: 99 - 100: 14.207 distance: 100 - 101: 15.977 distance: 100 - 102: 12.195 distance: 103 - 104: 11.723 distance: 104 - 105: 14.891 distance: 104 - 107: 37.285 distance: 105 - 106: 9.900 distance: 105 - 111: 40.654 distance: 107 - 108: 42.734 distance: 108 - 109: 24.654 distance: 108 - 110: 30.078 distance: 111 - 112: 25.497 distance: 112 - 113: 8.085 distance: 112 - 115: 23.612 distance: 113 - 114: 6.598 distance: 113 - 119: 11.900 distance: 115 - 116: 11.735 distance: 116 - 117: 16.491 distance: 116 - 118: 10.639 distance: 119 - 120: 9.843 distance: 120 - 121: 31.836 distance: 120 - 123: 10.478 distance: 121 - 122: 8.457 distance: 121 - 124: 6.223 distance: 124 - 125: 24.839 distance: 125 - 126: 10.484 distance: 125 - 128: 12.577 distance: 126 - 127: 41.534 distance: 126 - 135: 16.184 distance: 128 - 129: 28.692 distance: 129 - 130: 6.452 distance: 130 - 131: 21.235 distance: 131 - 132: 17.797 distance: 132 - 133: 16.936 distance: 132 - 134: 21.959 distance: 135 - 136: 9.023 distance: 136 - 137: 37.349 distance: 136 - 139: 26.483 distance: 137 - 138: 17.600 distance: 137 - 143: 26.223 distance: 139 - 140: 12.494 distance: 140 - 141: 15.157 distance: 140 - 142: 14.235 distance: 143 - 144: 40.101 distance: 143 - 149: 39.445 distance: 144 - 145: 39.544 distance: 144 - 147: 13.992 distance: 145 - 146: 36.174 distance: 145 - 150: 19.342 distance: 147 - 148: 11.944 distance: 148 - 149: 7.993 distance: 151 - 152: 4.236 distance: 151 - 154: 41.700 distance: 152 - 153: 34.749 distance: 152 - 156: 5.811 distance: 154 - 155: 43.178 distance: 156 - 157: 23.817 distance: 157 - 158: 14.875 distance: 157 - 160: 24.868 distance: 158 - 159: 26.378 distance: 158 - 167: 20.997 distance: 159 - 178: 24.657 distance: 160 - 161: 12.587 distance: 161 - 162: 21.772 distance: 161 - 163: 18.591 distance: 162 - 164: 21.714 distance: 163 - 165: 40.195 distance: 164 - 166: 29.749 distance: 165 - 166: 22.409