Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:00:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/11_2022/6uur_20900.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 1.94, per 1000 atoms: 0.70 Number of scatterers: 2770 At special positions: 0 Unit cell: (86.67, 58.85, 40.66, 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 40 16.00 O 490 8.00 N 500 7.00 C 1740 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: 1.05 Conformation dependent library (CDL) restraints added in 452.7 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 107 through 124 removed outlier: 6.498A pdb=" N THR D 107 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS H 110 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET D 109 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET H 112 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N HIS D 111 " --> pdb=" O MET H 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY H 114 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA D 113 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA H 116 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA D 115 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA H 118 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA D 117 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ALA H 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY D 119 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL H 122 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY H 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY D 123 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 107 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS D 110 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET A 109 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET D 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS A 111 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N GLY D 114 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA A 113 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA D 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA A 115 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA D 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 117 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA D 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 119 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL D 122 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY D 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 123 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET A 112 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA E 113 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 114 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET E 112 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 113 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY E 114 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 134 through 135 removed outlier: 6.634A pdb=" N MET D 134 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 134 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 138 through 140 removed outlier: 6.152A pdb=" N ILE A 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE E 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 107 through 124 removed outlier: 6.854A pdb=" N MET C 112 " --> pdb=" O HIS G 111 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA G 113 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY C 114 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 112 " --> pdb=" O HIS C 111 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA C 113 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY B 114 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 107 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS F 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET B 109 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET F 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS B 111 " --> pdb=" O MET F 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY F 114 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA B 113 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA F 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 115 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA F 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 117 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA F 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 119 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL F 122 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY F 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 123 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR F 107 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS J 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET F 109 " --> pdb=" O LYS J 110 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET J 112 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS F 111 " --> pdb=" O MET J 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY J 114 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA F 113 " --> pdb=" O GLY J 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA J 116 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA F 115 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA J 118 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 117 " --> pdb=" O ALA J 118 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ALA J 120 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY F 119 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL J 122 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 121 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY J 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY F 123 " --> pdb=" O GLY J 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.632A pdb=" N MET B 134 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET F 134 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 138 through 140 removed outlier: 6.176A pdb=" N ILE C 139 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 139 " --> pdb=" O HIS C 140 " (cutoff:3.500A) 69 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: 0.60 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 900 1.35 - 1.46: 650 1.46 - 1.58: 1190 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 2820 Sorted by residual: bond pdb=" CB MET C 112 " pdb=" CG MET C 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.30e-01 bond pdb=" CB MET F 112 " pdb=" CG MET F 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.30e-01 bond pdb=" CB MET H 112 " pdb=" CG MET H 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" CB MET B 112 " pdb=" CG MET B 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" CB MET D 112 " pdb=" CG MET D 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.26e-01 ... (remaining 2815 not shown) Histogram of bond angle deviations from ideal: 99.40 - 105.80: 66 105.80 - 112.19: 1394 112.19 - 118.59: 730 118.59 - 124.98: 1530 124.98 - 131.38: 40 Bond angle restraints: 3760 Sorted by residual: angle pdb=" CA LEU J 130 " pdb=" CB LEU J 130 " pdb=" CG LEU J 130 " ideal model delta sigma weight residual 116.30 122.72 -6.42 3.50e+00 8.16e-02 3.36e+00 angle pdb=" CA LEU H 130 " pdb=" CB LEU H 130 " pdb=" CG LEU H 130 " ideal model delta sigma weight residual 116.30 122.72 -6.42 3.50e+00 8.16e-02 3.36e+00 angle pdb=" CA LEU F 130 " pdb=" CB LEU F 130 " pdb=" CG LEU F 130 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 angle pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " pdb=" CG LEU C 130 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 angle pdb=" CA LEU G 130 " pdb=" CB LEU G 130 " pdb=" CG LEU G 130 " ideal model delta sigma weight residual 116.30 122.70 -6.40 3.50e+00 8.16e-02 3.35e+00 ... (remaining 3755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.18: 1130 8.18 - 16.36: 200 16.36 - 24.54: 130 24.54 - 32.72: 110 32.72 - 40.90: 40 Dihedral angle restraints: 1610 sinusoidal: 560 harmonic: 1050 Sorted by residual: dihedral pdb=" CA MET F 109 " pdb=" C MET F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta harmonic sigma weight residual -180.00 -164.95 -15.05 0 5.00e+00 4.00e-02 9.06e+00 dihedral pdb=" CA MET H 109 " pdb=" C MET H 109 " pdb=" N LYS H 110 " pdb=" CA LYS H 110 " ideal model delta harmonic sigma weight residual -180.00 -165.00 -15.00 0 5.00e+00 4.00e-02 9.00e+00 dihedral pdb=" CA MET C 109 " pdb=" C MET C 109 " pdb=" N LYS C 110 " pdb=" CA LYS C 110 " ideal model delta harmonic sigma weight residual -180.00 -165.00 -15.00 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.030: 206 0.030 - 0.056: 94 0.056 - 0.083: 34 0.083 - 0.109: 29 0.109 - 0.135: 27 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE E 139 " pdb=" N ILE E 139 " pdb=" C ILE E 139 " pdb=" CB ILE E 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE J 139 " pdb=" N ILE J 139 " pdb=" C ILE J 139 " pdb=" CB ILE J 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 387 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 141 " -0.005 2.00e-02 2.50e+03 3.48e-03 2.12e-01 pdb=" CG PHE J 141 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE J 141 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE J 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE J 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE J 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 141 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 141 " 0.005 2.00e-02 2.50e+03 3.42e-03 2.04e-01 pdb=" CG PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE H 141 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 141 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 141 " -0.004 2.00e-02 2.50e+03 3.28e-03 1.88e-01 pdb=" CG PHE C 141 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE C 141 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 141 " -0.005 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1589 3.09 - 3.55: 2685 3.55 - 4.00: 4124 4.00 - 4.45: 5058 4.45 - 4.90: 9474 Nonbonded interactions: 22930 Sorted by model distance: nonbonded pdb=" N GLY J 126 " pdb=" O GLY J 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY I 126 " pdb=" O GLY I 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY B 126 " pdb=" O GLY B 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY F 126 " pdb=" O GLY F 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY E 126 " pdb=" O GLY E 126 " model vdw 2.644 2.496 ... (remaining 22925 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 1740 2.51 5 N 500 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.000 Extract box with map and model: 12.360 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 13.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.024 2820 Z= 0.252 Angle : 0.760 6.416 3760 Z= 0.384 Chirality : 0.051 0.135 390 Planarity : 0.002 0.010 480 Dihedral : 15.648 40.900 970 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.23), residues: 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1449 time to fit residues: 15.3601 Evaluate side-chains 77 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 11 optimal weight: 6.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 108 ASN ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.044 2820 Z= 0.492 Angle : 0.915 6.249 3760 Z= 0.460 Chirality : 0.048 0.130 390 Planarity : 0.003 0.010 480 Dihedral : 5.358 19.922 420 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 7.60 % 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: -4.31 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.25), residues: 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.324 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 0.1230 time to fit residues: 12.9587 Evaluate side-chains 81 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0303 time to fit residues: 1.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 2820 Z= 0.331 Angle : 0.788 6.487 3760 Z= 0.399 Chirality : 0.047 0.131 390 Planarity : 0.002 0.008 480 Dihedral : 4.945 20.109 420 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 2.80 % 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: -4.22 (0.33), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.320 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 81 average time/residue: 0.1039 time to fit residues: 10.6139 Evaluate side-chains 74 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 2820 Z= 0.359 Angle : 0.795 5.888 3760 Z= 0.403 Chirality : 0.048 0.131 390 Planarity : 0.002 0.008 480 Dihedral : 4.986 19.353 420 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer Outliers : 6.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.323 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.1003 time to fit residues: 10.3503 Evaluate side-chains 79 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0308 time to fit residues: 0.8905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.062 2820 Z= 0.664 Angle : 1.015 6.602 3760 Z= 0.520 Chirality : 0.051 0.136 390 Planarity : 0.004 0.011 480 Dihedral : 5.756 19.453 420 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.24), residues: 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.322 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.1287 time to fit residues: 12.9558 Evaluate side-chains 82 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0295 time to fit residues: 0.7614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2820 Z= 0.224 Angle : 0.711 6.124 3760 Z= 0.365 Chirality : 0.048 0.135 390 Planarity : 0.002 0.018 480 Dihedral : 4.905 22.409 420 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 4.40 % 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: -4.38 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.24), residues: 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.311 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.1247 time to fit residues: 13.5592 Evaluate side-chains 88 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0289 time to fit residues: 0.7336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 2820 Z= 0.353 Angle : 0.808 5.953 3760 Z= 0.412 Chirality : 0.048 0.133 390 Planarity : 0.003 0.020 480 Dihedral : 5.048 19.029 420 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.24), residues: 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.326 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.1129 time to fit residues: 12.3156 Evaluate side-chains 84 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0364 time to fit residues: 0.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2820 Z= 0.215 Angle : 0.707 5.543 3760 Z= 0.359 Chirality : 0.048 0.130 390 Planarity : 0.002 0.017 480 Dihedral : 4.713 19.050 420 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 4.40 % 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: -4.49 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.24), residues: 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.324 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1178 time to fit residues: 13.3334 Evaluate side-chains 93 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0306 time to fit residues: 0.8649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2820 Z= 0.229 Angle : 0.718 6.695 3760 Z= 0.365 Chirality : 0.047 0.129 390 Planarity : 0.002 0.018 480 Dihedral : 4.689 17.846 420 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.24), residues: 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.330 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1319 time to fit residues: 14.3595 Evaluate side-chains 86 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0405 time to fit residues: 0.5853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 2820 Z= 0.356 Angle : 0.836 7.482 3760 Z= 0.423 Chirality : 0.048 0.130 390 Planarity : 0.003 0.017 480 Dihedral : 4.949 17.223 420 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 4.40 % 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: -4.57 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.24), residues: 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.1214 time to fit residues: 12.9222 Evaluate side-chains 90 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0560 time to fit residues: 1.1247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.154194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.128592 restraints weight = 3579.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.131212 restraints weight = 1970.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.132976 restraints weight = 1441.614| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 2820 Z= 0.432 Angle : 0.894 7.997 3760 Z= 0.457 Chirality : 0.050 0.132 390 Planarity : 0.003 0.018 480 Dihedral : 5.102 18.893 420 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer Outliers : 1.20 % 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: -4.61 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.24), residues: 380 =============================================================================== Job complete usr+sys time: 1162.26 seconds wall clock time: 21 minutes 34.87 seconds (1294.87 seconds total)