Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:55:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrq_0958/11_2022/6lrq_0958.pdb" } resolution = 3.49 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= 0.003 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: 2628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, per 1000 atoms: 0.72 Number of scatterers: 2628 At special positions: 0 Unit cell: (107.124, 109.836, 33.9, 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 528 8.00 N 456 7.00 C 1644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 421.9 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.775A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 83 removed outlier: 6.823A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 83 removed outlier: 6.823A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU C 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 96 removed outlier: 8.871A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LYS B 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY C 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 55 removed outlier: 6.809A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY E 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 83 removed outlier: 8.917A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N THR E 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU E 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLU F 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL E 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 88 through 96 removed outlier: 8.953A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY E 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N PHE F 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY E 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS F 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 34 hydrogen bonds defined for protein. 102 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: 0.52 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: 1.22 - 1.29: 462 1.29 - 1.35: 408 1.35 - 1.41: 102 1.41 - 1.48: 439 1.48 - 1.54: 1229 Bond restraints: 2640 Sorted by residual: bond pdb=" CB VAL B 77 " pdb=" CG1 VAL B 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 bond pdb=" CB VAL A 77 " pdb=" CG1 VAL A 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB VAL F 77 " pdb=" CG1 VAL F 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" CB VAL E 77 " pdb=" CG1 VAL E 77 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB VAL C 77 " pdb=" CG1 VAL C 77 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 106.18 - 111.18: 1178 111.18 - 116.18: 786 116.18 - 121.17: 792 121.17 - 126.17: 808 126.17 - 131.17: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N THR F 72 " pdb=" CA THR F 72 " pdb=" C THR F 72 " ideal model delta sigma weight residual 109.86 106.92 2.94 1.55e+00 4.16e-01 3.60e+00 angle pdb=" N THR D 72 " pdb=" CA THR D 72 " pdb=" C THR D 72 " ideal model delta sigma weight residual 109.86 106.93 2.93 1.55e+00 4.16e-01 3.57e+00 angle pdb=" C THR A 92 " pdb=" N GLY A 93 " pdb=" CA GLY A 93 " ideal model delta sigma weight residual 121.41 117.72 3.69 1.96e+00 2.60e-01 3.54e+00 angle pdb=" C THR F 92 " pdb=" N GLY F 93 " pdb=" CA GLY F 93 " ideal model delta sigma weight residual 121.41 117.73 3.68 1.96e+00 2.60e-01 3.53e+00 angle pdb=" C THR D 92 " pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 121.41 117.73 3.68 1.96e+00 2.60e-01 3.52e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.15: 1132 7.15 - 14.30: 224 14.30 - 21.44: 102 21.44 - 28.59: 47 28.59 - 35.74: 31 Dihedral angle restraints: 1536 sinusoidal: 522 harmonic: 1014 Sorted by residual: dihedral pdb=" CA LEU C 38 " pdb=" C LEU C 38 " pdb=" N TYR C 39 " pdb=" CA TYR C 39 " ideal model delta harmonic sigma weight residual 180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 dihedral pdb=" CA LEU E 38 " pdb=" C LEU E 38 " pdb=" N TYR E 39 " pdb=" CA TYR E 39 " ideal model delta harmonic sigma weight residual 180.00 -164.88 -15.12 0 5.00e+00 4.00e-02 9.15e+00 dihedral pdb=" CA LEU F 38 " pdb=" C LEU F 38 " pdb=" N TYR F 39 " pdb=" CA TYR F 39 " ideal model delta harmonic sigma weight residual -180.00 -164.88 -15.12 0 5.00e+00 4.00e-02 9.14e+00 ... (remaining 1533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 173 0.026 - 0.052: 170 0.052 - 0.079: 61 0.079 - 0.105: 42 0.105 - 0.131: 22 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL E 55 " pdb=" N VAL E 55 " pdb=" C VAL E 55 " pdb=" CB VAL E 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL B 55 " pdb=" N VAL B 55 " pdb=" C VAL B 55 " pdb=" CB VAL B 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL D 55 " pdb=" N VAL D 55 " pdb=" C VAL D 55 " pdb=" CB VAL D 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.010 2.00e-02 2.50e+03 8.12e-03 1.15e+00 pdb=" CG PHE E 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.010 2.00e-02 2.50e+03 8.00e-03 1.12e+00 pdb=" CG PHE B 94 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " -0.009 2.00e-02 2.50e+03 8.00e-03 1.12e+00 pdb=" CG PHE C 94 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 345 2.74 - 3.28: 2948 3.28 - 3.82: 3970 3.82 - 4.36: 4253 4.36 - 4.90: 8364 Nonbonded interactions: 19880 Sorted by model distance: nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.205 2.520 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.207 2.520 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.207 2.520 nonbonded pdb=" ND2 ASN E 65 " pdb=" O GLY E 68 " model vdw 2.207 2.520 nonbonded pdb=" ND2 ASN B 65 " pdb=" O GLY B 68 " model vdw 2.207 2.520 ... (remaining 19875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1644 2.51 5 N 456 2.21 5 O 528 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 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: 1.010 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: 4.780 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.810 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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 : 0.009 0.044 2640 Z= 0.603 Angle : 0.850 6.409 3570 Z= 0.470 Chirality : 0.051 0.131 468 Planarity : 0.003 0.011 444 Dihedral : 11.881 35.739 900 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % 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: -4.51 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.22), residues: 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.323 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1299 time to fit residues: 9.6437 Evaluate side-chains 47 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7005 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2640 Z= 0.236 Angle : 0.589 5.391 3570 Z= 0.323 Chirality : 0.048 0.158 468 Planarity : 0.002 0.008 444 Dihedral : 5.039 14.902 378 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer Outliers : 10.00 % 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: -3.68 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.25), residues: 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 0.328 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 86 average time/residue: 0.1018 time to fit residues: 11.1109 Evaluate side-chains 76 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0270 time to fit residues: 1.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 2640 Z= 0.439 Angle : 0.759 9.374 3570 Z= 0.407 Chirality : 0.050 0.143 468 Planarity : 0.003 0.009 444 Dihedral : 6.071 22.201 378 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.13 % Favored : 80.87 % Rotamer Outliers : 8.15 % 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: -3.62 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 0.317 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.0951 time to fit residues: 8.3017 Evaluate side-chains 61 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0284 time to fit residues: 1.0778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.6893 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 2640 Z= 0.144 Angle : 0.529 6.365 3570 Z= 0.287 Chirality : 0.047 0.153 468 Planarity : 0.002 0.010 444 Dihedral : 4.650 15.402 378 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 5.93 % 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: -3.39 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0986 time to fit residues: 10.9022 Evaluate side-chains 76 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0270 time to fit residues: 1.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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: 0.6901 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2640 Z= 0.187 Angle : 0.583 7.521 3570 Z= 0.308 Chirality : 0.045 0.124 468 Planarity : 0.002 0.012 444 Dihedral : 4.819 20.344 378 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer Outliers : 3.70 % 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: -3.31 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.346 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.1012 time to fit residues: 8.6922 Evaluate side-chains 63 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0324 time to fit residues: 0.7578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.6970 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 2640 Z= 0.340 Angle : 0.687 7.958 3570 Z= 0.365 Chirality : 0.047 0.130 468 Planarity : 0.003 0.012 444 Dihedral : 5.584 24.445 378 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer Outliers : 5.19 % 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: -3.25 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.328 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.1014 time to fit residues: 8.6376 Evaluate side-chains 69 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0294 time to fit residues: 0.9958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.6851 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 2640 Z= 0.144 Angle : 0.564 7.719 3570 Z= 0.292 Chirality : 0.046 0.123 468 Planarity : 0.002 0.011 444 Dihedral : 4.601 19.729 378 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer Outliers : 2.22 % 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 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.0977 time to fit residues: 8.3955 Evaluate side-chains 63 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0262 time to fit residues: 0.5898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.6912 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2640 Z= 0.243 Angle : 0.609 8.168 3570 Z= 0.321 Chirality : 0.046 0.124 468 Planarity : 0.002 0.009 444 Dihedral : 4.984 21.446 378 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer Outliers : 2.59 % 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: -3.10 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.286 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.1017 time to fit residues: 7.7745 Evaluate side-chains 65 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0256 time to fit residues: 0.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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: 0.6764 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 2640 Z= 0.119 Angle : 0.523 6.985 3570 Z= 0.273 Chirality : 0.045 0.122 468 Planarity : 0.002 0.009 444 Dihedral : 4.110 16.178 378 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.74 % 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 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.27), residues: 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.311 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.1054 time to fit residues: 9.3463 Evaluate side-chains 63 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 2640 Z= 0.237 Angle : 0.641 9.051 3570 Z= 0.327 Chirality : 0.046 0.121 468 Planarity : 0.003 0.025 444 Dihedral : 4.681 19.519 378 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.27), residues: 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.311 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 61 average time/residue: 0.1092 time to fit residues: 8.3537 Evaluate side-chains 56 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.212389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.193908 restraints weight = 5692.164| |-----------------------------------------------------------------------------| r_work (start): 0.4822 rms_B_bonded: 2.65 r_work: 0.4814 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4807 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.4801 rms_B_bonded: 2.38 restraints_weight: 0.1250 r_work: 0.4793 rms_B_bonded: 2.48 restraints_weight: 0.0625 r_work: 0.4785 rms_B_bonded: 2.63 restraints_weight: 0.0312 r_work: 0.4775 rms_B_bonded: 2.82 restraints_weight: 0.0156 r_work: 0.4764 rms_B_bonded: 3.08 restraints_weight: 0.0078 r_work: 0.4752 rms_B_bonded: 3.40 restraints_weight: 0.0039 r_work: 0.4738 rms_B_bonded: 3.81 restraints_weight: 0.0020 r_work: 0.4721 rms_B_bonded: 4.32 restraints_weight: 0.0010 r_work: 0.4701 rms_B_bonded: 4.96 restraints_weight: 0.0005 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.033 2640 Z= 0.402 Angle : 0.771 9.444 3570 Z= 0.405 Chirality : 0.048 0.146 468 Planarity : 0.003 0.024 444 Dihedral : 5.601 22.187 378 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer Outliers : 0.74 % 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: -3.04 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 366 =============================================================================== Job complete usr+sys time: 959.80 seconds wall clock time: 18 minutes 56.99 seconds (1136.99 seconds total)