Starting phenix.real_space_refine on Tue Feb 13 04:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/02_2024/7yk8_33890.pdb" } resolution = 2.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1938 2.51 5 N 546 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 98": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 2.06, per 1000 atoms: 0.66 Number of scatterers: 3108 At special positions: 0 Unit cell: (94.34, 117.66, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 624 8.00 N 546 7.00 C 1938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 668.2 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 57 removed outlier: 6.878A pdb=" N VAL J 48 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL L 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS J 50 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY L 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLU L 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL K 49 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL L 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N GLY K 51 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS L 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ALA K 53 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL L 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL K 55 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR L 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU K 57 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA L 56 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 61 through 66 removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASN J 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR L 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 69 through 82 removed outlier: 6.597A pdb=" N ALA L 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR J 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL L 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL J 74 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY L 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ALA J 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR L 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA J 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL L 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LYS J 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN L 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL J 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR L 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL L 74 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR K 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA L 76 " --> pdb=" O THR K 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 86 through 92 removed outlier: 6.976A pdb=" N SER L 87 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE J 88 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLY L 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N ALA K 89 " --> pdb=" O GLY L 86 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE L 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA K 91 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA L 90 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 16 through 18 removed outlier: 6.225A pdb=" N VAL I 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 57 removed outlier: 6.883A pdb=" N VAL E 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS E 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY B 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.310A pdb=" N GLN B 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN E 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82 removed outlier: 6.598A pdb=" N ALA B 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR E 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY B 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ALA E 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ALA E 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS E 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN B 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL E 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR B 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 74 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR F 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92 removed outlier: 6.980A pdb=" N SER B 87 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY B 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ALA F 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.220A pdb=" N VAL A 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 552 1.29 - 1.35: 482 1.35 - 1.42: 106 1.42 - 1.48: 498 1.48 - 1.55: 1476 Bond restraints: 3114 Sorted by residual: bond pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.50e+00 bond pdb=" N LEU L 38 " pdb=" CA LEU L 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU J 38 " pdb=" CA LEU J 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU K 38 " pdb=" CA LEU K 38 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.26e+00 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 105.90 - 110.97: 1263 110.97 - 116.04: 970 116.04 - 121.10: 938 121.10 - 126.17: 1017 126.17 - 131.23: 6 Bond angle restraints: 4194 Sorted by residual: angle pdb=" N LEU L 38 " pdb=" CA LEU L 38 " pdb=" C LEU L 38 " ideal model delta sigma weight residual 112.93 108.91 4.02 1.33e+00 5.65e-01 9.12e+00 angle pdb=" N LEU E 38 " pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 112.93 108.92 4.01 1.33e+00 5.65e-01 9.08e+00 angle pdb=" N LEU F 38 " pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 112.93 108.93 4.00 1.33e+00 5.65e-01 9.04e+00 angle pdb=" N LEU K 38 " pdb=" CA LEU K 38 " pdb=" C LEU K 38 " ideal model delta sigma weight residual 112.93 108.94 3.99 1.33e+00 5.65e-01 9.01e+00 angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 112.93 108.96 3.97 1.33e+00 5.65e-01 8.92e+00 ... (remaining 4189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 1572 10.91 - 21.82: 192 21.82 - 32.73: 48 32.73 - 43.63: 12 43.63 - 54.54: 12 Dihedral angle restraints: 1836 sinusoidal: 624 harmonic: 1212 Sorted by residual: dihedral pdb=" N LYS F 45 " pdb=" CA LYS F 45 " pdb=" CB LYS F 45 " pdb=" CG LYS F 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS J 45 " pdb=" CA LYS J 45 " pdb=" CB LYS J 45 " pdb=" CG LYS J 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS L 45 " pdb=" CA LYS L 45 " pdb=" CB LYS L 45 " pdb=" CG LYS L 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.47 -54.53 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 261 0.033 - 0.067: 150 0.067 - 0.100: 50 0.100 - 0.134: 61 0.134 - 0.167: 24 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL L 37 " pdb=" N VAL L 37 " pdb=" C VAL L 37 " pdb=" CB VAL L 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 543 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 95 " -0.004 2.00e-02 2.50e+03 7.83e-03 6.13e-01 pdb=" C VAL L 95 " 0.014 2.00e-02 2.50e+03 pdb=" O VAL L 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS L 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 95 " -0.004 2.00e-02 2.50e+03 7.80e-03 6.09e-01 pdb=" C VAL J 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL J 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS J 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 95 " -0.004 2.00e-02 2.50e+03 7.73e-03 5.97e-01 pdb=" C VAL F 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL F 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS F 96 " -0.004 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1354 2.95 - 3.44: 2895 3.44 - 3.93: 4431 3.93 - 4.41: 4982 4.41 - 4.90: 10182 Nonbonded interactions: 23844 Sorted by model distance: nonbonded pdb=" N VAL B 37 " pdb=" O VAL F 37 " model vdw 2.465 2.520 nonbonded pdb=" N VAL L 37 " pdb=" O VAL K 37 " model vdw 2.480 2.520 nonbonded pdb=" O VAL L 37 " pdb=" N VAL J 37 " model vdw 2.488 2.520 nonbonded pdb=" O VAL B 37 " pdb=" N VAL E 37 " model vdw 2.495 2.520 nonbonded pdb=" O ILE B 88 " pdb=" N ALA F 89 " model vdw 2.650 2.520 ... (remaining 23839 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 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 4.800 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.005 0.036 3114 Z= 0.320 Angle : 0.661 4.016 4194 Z= 0.415 Chirality : 0.063 0.167 546 Planarity : 0.002 0.008 522 Dihedral : 11.560 54.540 1068 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 50 PHE 0.011 0.003 PHE K 94 TYR 0.004 0.001 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.302 Fit side-chains REVERT: A 20 GLU cc_start: 0.7565 (tt0) cc_final: 0.7271 (tt0) REVERT: J 60 LYS cc_start: 0.8416 (tttt) cc_final: 0.8130 (tmtm) REVERT: G 20 GLU cc_start: 0.7482 (tt0) cc_final: 0.7044 (tt0) REVERT: E 43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7288 (mmmm) REVERT: C 20 GLU cc_start: 0.7548 (tt0) cc_final: 0.7217 (tt0) REVERT: K 43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7087 (mmmm) REVERT: F 43 LYS cc_start: 0.7536 (tppp) cc_final: 0.7163 (mmmt) REVERT: F 45 LYS cc_start: 0.8026 (tttt) cc_final: 0.7791 (ttmt) REVERT: D 20 GLU cc_start: 0.7446 (tt0) cc_final: 0.7127 (tm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.0123 time to fit residues: 91.6857 Evaluate side-chains 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0010 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 65 ASN J 50 HIS E 50 HIS K 65 ASN F 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3114 Z= 0.279 Angle : 0.577 3.584 4194 Z= 0.336 Chirality : 0.054 0.148 546 Planarity : 0.002 0.012 522 Dihedral : 4.655 12.030 444 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 11.22 % Allowed : 10.90 % Favored : 77.88 % 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 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 50 PHE 0.011 0.003 PHE F 94 TYR 0.012 0.003 TYR K 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 0.481 Fit side-chains REVERT: B 45 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7586 (tttp) REVERT: A 20 GLU cc_start: 0.7587 (tt0) cc_final: 0.7311 (tt0) REVERT: J 60 LYS cc_start: 0.8434 (tttt) cc_final: 0.8144 (tmtm) REVERT: G 20 GLU cc_start: 0.7541 (tt0) cc_final: 0.7082 (tt0) REVERT: C 20 GLU cc_start: 0.7562 (tt0) cc_final: 0.7246 (tt0) REVERT: F 43 LYS cc_start: 0.7464 (tppp) cc_final: 0.7081 (mmmt) outliers start: 35 outliers final: 23 residues processed: 87 average time/residue: 1.0465 time to fit residues: 93.6747 Evaluate side-chains 101 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3114 Z= 0.381 Angle : 0.642 4.090 4194 Z= 0.378 Chirality : 0.055 0.153 546 Planarity : 0.002 0.013 522 Dihedral : 4.824 12.897 444 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 12.50 % Allowed : 14.10 % Favored : 73.40 % 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: -3.30 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.010 0.003 PHE K 94 TYR 0.015 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 80 time to evaluate : 0.344 Fit side-chains REVERT: L 60 LYS cc_start: 0.8386 (tmtp) cc_final: 0.8171 (ttpp) REVERT: B 60 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8165 (tmtp) REVERT: A 20 GLU cc_start: 0.7586 (tt0) cc_final: 0.7265 (tt0) REVERT: J 60 LYS cc_start: 0.8422 (tttt) cc_final: 0.8140 (tmtm) REVERT: G 20 GLU cc_start: 0.7532 (tt0) cc_final: 0.7091 (tt0) REVERT: E 60 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7856 (tmtp) REVERT: C 20 GLU cc_start: 0.7561 (tt0) cc_final: 0.7243 (tt0) REVERT: F 43 LYS cc_start: 0.7539 (tppp) cc_final: 0.7120 (mmmt) REVERT: F 83 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7437 (mt-10) outliers start: 39 outliers final: 25 residues processed: 87 average time/residue: 1.0779 time to fit residues: 96.4156 Evaluate side-chains 105 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.222 Angle : 0.529 3.857 4194 Z= 0.309 Chirality : 0.052 0.138 546 Planarity : 0.002 0.012 522 Dihedral : 4.510 12.922 444 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 13.78 % Allowed : 13.46 % Favored : 72.76 % 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: -3.08 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 50 PHE 0.011 0.003 PHE K 94 TYR 0.009 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 0.344 Fit side-chains REVERT: L 60 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: B 45 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7925 (ttmt) REVERT: B 60 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8051 (tmtp) REVERT: A 20 GLU cc_start: 0.7515 (tt0) cc_final: 0.7224 (tt0) REVERT: J 60 LYS cc_start: 0.8408 (tttt) cc_final: 0.8158 (tmtm) REVERT: G 20 GLU cc_start: 0.7554 (tt0) cc_final: 0.7120 (tt0) REVERT: E 38 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6377 (tt) REVERT: E 60 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7820 (tmtp) REVERT: C 20 GLU cc_start: 0.7558 (tt0) cc_final: 0.7251 (tt0) REVERT: K 60 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7691 (tmtp) REVERT: F 43 LYS cc_start: 0.7538 (tppp) cc_final: 0.7097 (mmmt) REVERT: F 83 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7374 (mt-10) outliers start: 43 outliers final: 23 residues processed: 94 average time/residue: 0.9899 time to fit residues: 95.8372 Evaluate side-chains 107 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3114 Z= 0.302 Angle : 0.590 3.944 4194 Z= 0.348 Chirality : 0.054 0.147 546 Planarity : 0.002 0.014 522 Dihedral : 4.637 14.360 444 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 13.46 % Allowed : 13.14 % Favored : 73.40 % 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: -3.12 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.011 0.003 PHE F 94 TYR 0.011 0.003 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 83 time to evaluate : 0.367 Fit side-chains REVERT: L 60 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (ttpp) REVERT: B 38 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5818 (tt) REVERT: B 60 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8087 (tmtp) REVERT: A 20 GLU cc_start: 0.7521 (tt0) cc_final: 0.7239 (tt0) REVERT: J 43 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6825 (mmmm) REVERT: J 60 LYS cc_start: 0.8403 (tttt) cc_final: 0.8149 (tmtm) REVERT: G 20 GLU cc_start: 0.7569 (tt0) cc_final: 0.7111 (tt0) REVERT: E 60 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7821 (tmtp) REVERT: C 20 GLU cc_start: 0.7561 (tt0) cc_final: 0.7247 (tt0) REVERT: K 60 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7670 (tmtp) REVERT: F 38 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6512 (tm) REVERT: F 43 LYS cc_start: 0.7626 (tppp) cc_final: 0.7138 (mmmt) REVERT: F 83 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7348 (mt-10) outliers start: 42 outliers final: 26 residues processed: 92 average time/residue: 0.9960 time to fit residues: 94.3223 Evaluate side-chains 114 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 62 GLN K 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3114 Z= 0.232 Angle : 0.545 4.839 4194 Z= 0.319 Chirality : 0.052 0.140 546 Planarity : 0.002 0.012 522 Dihedral : 4.537 14.446 444 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 12.18 % Allowed : 14.42 % Favored : 73.40 % 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: -3.01 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 50 PHE 0.011 0.003 PHE F 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 0.377 Fit side-chains REVERT: L 60 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8161 (ttpp) REVERT: B 38 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5891 (tt) REVERT: B 60 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8025 (tmtp) REVERT: A 20 GLU cc_start: 0.7512 (tt0) cc_final: 0.7217 (tt0) REVERT: J 60 LYS cc_start: 0.8392 (tttt) cc_final: 0.8147 (tmtm) REVERT: G 20 GLU cc_start: 0.7561 (tt0) cc_final: 0.7094 (tt0) REVERT: C 20 GLU cc_start: 0.7551 (tt0) cc_final: 0.7241 (tt0) REVERT: K 60 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7678 (tmtp) REVERT: F 38 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6488 (tm) REVERT: F 43 LYS cc_start: 0.7650 (tppp) cc_final: 0.7154 (mmmt) REVERT: F 83 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 20 GLU cc_start: 0.7377 (tt0) cc_final: 0.7018 (tt0) outliers start: 38 outliers final: 25 residues processed: 89 average time/residue: 0.9748 time to fit residues: 89.4137 Evaluate side-chains 111 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS B 65 ASN E 62 GLN K 65 ASN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 3114 Z= 0.464 Angle : 0.740 9.698 4194 Z= 0.428 Chirality : 0.058 0.159 546 Planarity : 0.003 0.018 522 Dihedral : 4.989 13.774 444 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 12.50 % Allowed : 14.10 % Favored : 73.40 % 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: -3.22 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS L 50 PHE 0.011 0.003 PHE L 94 TYR 0.016 0.004 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 80 time to evaluate : 0.351 Fit side-chains REVERT: L 60 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: L 61 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: L 62 GLN cc_start: 0.7713 (tt0) cc_final: 0.7482 (tt0) REVERT: B 38 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5778 (tt) REVERT: B 60 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8115 (tmtp) REVERT: A 20 GLU cc_start: 0.7408 (tt0) cc_final: 0.7083 (tt0) REVERT: J 43 LYS cc_start: 0.7338 (mmtt) cc_final: 0.6845 (mmmm) REVERT: J 60 LYS cc_start: 0.8412 (tttt) cc_final: 0.8151 (tmtm) REVERT: G 20 GLU cc_start: 0.7517 (tt0) cc_final: 0.7047 (tt0) REVERT: C 20 GLU cc_start: 0.7542 (tt0) cc_final: 0.7227 (tt0) REVERT: K 60 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7646 (tmtp) REVERT: F 43 LYS cc_start: 0.7638 (tppp) cc_final: 0.7172 (mmmt) outliers start: 39 outliers final: 27 residues processed: 90 average time/residue: 1.0678 time to fit residues: 98.7892 Evaluate side-chains 109 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.145 Angle : 0.526 10.181 4194 Z= 0.290 Chirality : 0.051 0.137 546 Planarity : 0.002 0.009 522 Dihedral : 4.423 14.891 444 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.41 % Allowed : 20.51 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 50 PHE 0.011 0.003 PHE B 94 TYR 0.005 0.001 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.357 Fit side-chains REVERT: L 43 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6911 (mmtt) REVERT: L 60 LYS cc_start: 0.8428 (tmtp) cc_final: 0.8119 (ttpp) REVERT: L 80 LYS cc_start: 0.8626 (tttm) cc_final: 0.8394 (tttt) REVERT: A 20 GLU cc_start: 0.7502 (tt0) cc_final: 0.7243 (tt0) REVERT: J 60 LYS cc_start: 0.8402 (tttt) cc_final: 0.8172 (tmtm) REVERT: G 20 GLU cc_start: 0.7542 (tt0) cc_final: 0.7078 (tt0) REVERT: E 60 LYS cc_start: 0.8430 (tmtp) cc_final: 0.7999 (tmtm) REVERT: C 20 GLU cc_start: 0.7556 (tt0) cc_final: 0.7231 (tt0) REVERT: F 43 LYS cc_start: 0.7657 (tppp) cc_final: 0.7163 (mmmt) REVERT: D 20 GLU cc_start: 0.7360 (tt0) cc_final: 0.6988 (tt0) outliers start: 20 outliers final: 16 residues processed: 89 average time/residue: 0.9492 time to fit residues: 87.1118 Evaluate side-chains 95 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0040 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3114 Z= 0.329 Angle : 0.666 9.223 4194 Z= 0.377 Chirality : 0.055 0.148 546 Planarity : 0.002 0.017 522 Dihedral : 4.752 15.146 444 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 9.29 % Allowed : 18.91 % Favored : 71.79 % 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: -3.02 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS J 50 PHE 0.011 0.003 PHE L 94 TYR 0.013 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 0.382 Fit side-chains REVERT: L 60 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8092 (ttpp) REVERT: L 61 GLU cc_start: 0.7339 (tp30) cc_final: 0.6982 (tp30) REVERT: A 20 GLU cc_start: 0.7592 (tt0) cc_final: 0.7261 (tt0) REVERT: J 43 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6796 (mmmm) REVERT: J 60 LYS cc_start: 0.8419 (tttt) cc_final: 0.8107 (tmtm) REVERT: G 20 GLU cc_start: 0.7552 (tt0) cc_final: 0.7080 (tt0) REVERT: E 40 VAL cc_start: 0.7732 (p) cc_final: 0.7527 (m) REVERT: C 20 GLU cc_start: 0.7559 (tt0) cc_final: 0.7241 (tt0) REVERT: F 43 LYS cc_start: 0.7633 (tppp) cc_final: 0.7156 (mmmt) REVERT: D 20 GLU cc_start: 0.7380 (tt0) cc_final: 0.7017 (tt0) outliers start: 29 outliers final: 25 residues processed: 88 average time/residue: 1.0960 time to fit residues: 99.1334 Evaluate side-chains 105 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3114 Z= 0.191 Angle : 0.611 10.150 4194 Z= 0.328 Chirality : 0.052 0.136 546 Planarity : 0.002 0.010 522 Dihedral : 4.606 15.922 444 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 7.69 % Allowed : 20.51 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 50 PHE 0.011 0.003 PHE F 94 TYR 0.007 0.001 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.318 Fit side-chains REVERT: L 60 LYS cc_start: 0.8362 (tmtp) cc_final: 0.8055 (ttpp) REVERT: L 61 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 20 GLU cc_start: 0.7513 (tt0) cc_final: 0.7254 (tt0) REVERT: J 60 LYS cc_start: 0.8484 (tttt) cc_final: 0.8223 (tmtm) REVERT: G 20 GLU cc_start: 0.7539 (tt0) cc_final: 0.7070 (tt0) REVERT: E 40 VAL cc_start: 0.7571 (p) cc_final: 0.7358 (m) REVERT: E 60 LYS cc_start: 0.8433 (tmtp) cc_final: 0.8026 (tmtm) REVERT: E 62 GLN cc_start: 0.7622 (mt0) cc_final: 0.7402 (tt0) REVERT: C 20 GLU cc_start: 0.7564 (tt0) cc_final: 0.7234 (tt0) REVERT: F 43 LYS cc_start: 0.7690 (tppp) cc_final: 0.7208 (mmmt) REVERT: D 20 GLU cc_start: 0.7374 (tt0) cc_final: 0.6989 (tt0) outliers start: 24 outliers final: 21 residues processed: 88 average time/residue: 1.0036 time to fit residues: 90.9149 Evaluate side-chains 100 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN K 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.196048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.152736 restraints weight = 2980.351| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.28 r_work: 0.3958 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.192 Angle : 0.621 10.106 4194 Z= 0.328 Chirality : 0.052 0.134 546 Planarity : 0.002 0.012 522 Dihedral : 4.469 16.428 444 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 7.69 % Allowed : 21.79 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 50 PHE 0.011 0.003 PHE K 94 TYR 0.009 0.002 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.68 seconds wall clock time: 35 minutes 13.39 seconds (2113.39 seconds total)