Starting phenix.real_space_refine on Thu Dec 7 16:27:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v47_31702/12_2023/7v47_31702.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v47_31702/12_2023/7v47_31702.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/7v47_31702/12_2023/7v47_31702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v47_31702/12_2023/7v47_31702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v47_31702/12_2023/7v47_31702.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v47_31702/12_2023/7v47_31702.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= 0.002 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 1554 2.51 5 N 432 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2484 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.70 Number of scatterers: 2484 At special positions: 0 Unit cell: (76.32, 111.3, 33.92, 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 498 8.00 N 432 7.00 C 1554 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: 0.92 Conformation dependent library (CDL) restraints added in 488.7 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.391A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.613A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.613A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY D 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA D 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL C 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N VAL D 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.029A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.395A pdb=" N TYR B 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER E 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER F 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.609A pdb=" N VAL B 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY E 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N HIS B 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N VAL B 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL E 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR B 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.035A pdb=" N GLU B 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR E 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL E 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN B 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU E 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR F 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL F 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN E 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 No hydrogen bonds 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: 0.06 Time building geometry restraints manager: 1.00 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: 432 1.29 - 1.35: 396 1.35 - 1.42: 96 1.42 - 1.48: 421 1.48 - 1.55: 1151 Bond restraints: 2496 Sorted by residual: bond pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.04e+00 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N THR E 72 " pdb=" CA THR E 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR F 72 " pdb=" CA THR F 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR A 72 " pdb=" CA THR A 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.90e+00 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 105.77 - 110.87: 973 110.87 - 115.96: 792 115.96 - 121.06: 841 121.06 - 126.15: 766 126.15 - 131.25: 6 Bond angle restraints: 3378 Sorted by residual: angle pdb=" CA THR A 72 " pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.41e+00 angle pdb=" CA THR B 72 " pdb=" CB THR B 72 " pdb=" CG2 THR B 72 " ideal model delta sigma weight residual 110.50 114.42 -3.92 1.70e+00 3.46e-01 5.31e+00 angle pdb=" CA THR D 72 " pdb=" CB THR D 72 " pdb=" CG2 THR D 72 " ideal model delta sigma weight residual 110.50 114.41 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA THR E 72 " pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 110.50 114.40 -3.90 1.70e+00 3.46e-01 5.26e+00 angle pdb=" CA THR F 72 " pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 110.50 114.39 -3.89 1.70e+00 3.46e-01 5.24e+00 ... (remaining 3373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1302 15.65 - 31.29: 126 31.29 - 46.94: 6 46.94 - 62.58: 0 62.58 - 78.23: 6 Dihedral angle restraints: 1440 sinusoidal: 462 harmonic: 978 Sorted by residual: dihedral pdb=" CA VAL E 49 " pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 dihedral pdb=" CA VAL C 49 " pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA VAL D 49 " pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta harmonic sigma weight residual 180.00 165.33 14.67 0 5.00e+00 4.00e-02 8.60e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 208 0.037 - 0.072: 140 0.072 - 0.108: 63 0.108 - 0.144: 27 0.144 - 0.180: 6 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA THR F 72 " pdb=" N THR F 72 " pdb=" C THR F 72 " pdb=" CB THR F 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA THR C 72 " pdb=" N THR C 72 " pdb=" C THR C 72 " pdb=" CB THR C 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA THR A 72 " pdb=" N THR A 72 " pdb=" C THR A 72 " pdb=" CB THR A 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 441 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE A 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.013 2.00e-02 2.50e+03 9.94e-03 1.73e+00 pdb=" CG PHE C 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.013 2.00e-02 2.50e+03 9.93e-03 1.72e+00 pdb=" CG PHE E 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.002 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 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.003 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1499 3.03 - 3.50: 2171 3.50 - 3.97: 3296 3.97 - 4.43: 3729 4.43 - 4.90: 6432 Nonbonded interactions: 17127 Sorted by model distance: nonbonded pdb=" OG1 THR C 44 " pdb=" N LYS C 45 " model vdw 2.567 2.520 nonbonded pdb=" OG1 THR D 44 " pdb=" N LYS D 45 " model vdw 2.567 2.520 nonbonded pdb=" OG1 THR F 44 " pdb=" N LYS F 45 " model vdw 2.567 2.520 nonbonded pdb=" OG1 THR A 44 " pdb=" N LYS A 45 " model vdw 2.568 2.520 nonbonded pdb=" OG1 THR E 44 " pdb=" N LYS E 45 " model vdw 2.568 2.520 ... (remaining 17122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.330 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: 6.430 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.010 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.007 0.030 2496 Z= 0.339 Angle : 0.781 4.148 3378 Z= 0.465 Chirality : 0.060 0.180 444 Planarity : 0.003 0.010 420 Dihedral : 12.908 78.231 828 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % Rotamer: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.86 (0.28), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.21), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.022 0.007 PHE A 94 TYR 0.006 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.8800 time to fit residues: 60.6414 Evaluate side-chains 57 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3621 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- 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: 0.7584 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2496 Z= 0.104 Angle : 0.550 4.808 3378 Z= 0.305 Chirality : 0.055 0.179 444 Planarity : 0.001 0.007 420 Dihedral : 4.434 15.344 366 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 5.69 % Allowed : 23.58 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.28), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.21), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.006 0.001 PHE D 94 TYR 0.013 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.276 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.8814 time to fit residues: 58.0689 Evaluate side-chains 64 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0514 time to fit residues: 0.7275 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN C 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2496 Z= 0.286 Angle : 0.739 6.796 3378 Z= 0.419 Chirality : 0.061 0.244 444 Planarity : 0.003 0.010 420 Dihedral : 5.695 14.126 366 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 21.19 % Favored : 78.53 % Rotamer: Outliers : 7.32 % Allowed : 23.98 % Favored : 68.70 % 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: -5.14 (0.30), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.022 0.006 PHE B 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.246 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 67 average time/residue: 0.9466 time to fit residues: 65.1089 Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0404 time to fit residues: 0.6956 ------------------------------------------------------------------------------- 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: 4.9990 chunk 3 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6116 ------------------------------------------------------------------------------- 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: 0.7589 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2496 Z= 0.123 Angle : 0.565 4.786 3378 Z= 0.314 Chirality : 0.055 0.182 444 Planarity : 0.001 0.008 420 Dihedral : 4.333 14.170 366 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 5.69 % Allowed : 26.42 % Favored : 67.89 % 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: -4.63 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.270 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 68 average time/residue: 0.8919 time to fit residues: 62.3942 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0442 time to fit residues: 0.6841 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 0.0170 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.9422 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2496 Z= 0.245 Angle : 0.688 6.238 3378 Z= 0.387 Chirality : 0.060 0.235 444 Planarity : 0.002 0.010 420 Dihedral : 5.321 13.758 366 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.19 % Favored : 78.81 % Rotamer: Outliers : 5.69 % Allowed : 29.67 % Favored : 64.63 % 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: -4.76 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.018 0.005 PHE F 94 TYR 0.014 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.273 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.9214 time to fit residues: 61.5829 Evaluate side-chains 70 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.4826 time to fit residues: 3.8373 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 33 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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: 0.7588 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2496 Z= 0.128 Angle : 0.573 5.014 3378 Z= 0.317 Chirality : 0.055 0.190 444 Planarity : 0.001 0.009 420 Dihedral : 4.333 14.314 366 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.66 % Allowed : 31.71 % Favored : 64.63 % 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: -4.32 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.013 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.270 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.8656 time to fit residues: 59.7182 Evaluate side-chains 64 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.0459 time to fit residues: 0.6085 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 2496 Z= 0.308 Angle : 0.771 7.255 3378 Z= 0.434 Chirality : 0.063 0.264 444 Planarity : 0.003 0.011 420 Dihedral : 5.770 14.380 366 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.03 % Favored : 77.97 % Rotamer: Outliers : 6.50 % Allowed : 28.05 % Favored : 65.45 % 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: -4.68 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.023 0.006 PHE F 94 TYR 0.013 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.245 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.8696 time to fit residues: 59.0515 Evaluate side-chains 67 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.0257 time to fit residues: 0.4820 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.0770 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2496 Z= 0.123 Angle : 0.575 4.847 3378 Z= 0.317 Chirality : 0.055 0.188 444 Planarity : 0.001 0.010 420 Dihedral : 4.365 14.968 366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 5.69 % Allowed : 28.86 % Favored : 65.45 % 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: -4.12 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.273 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.7901 time to fit residues: 54.6700 Evaluate side-chains 66 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0380 time to fit residues: 0.5331 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2496 Z= 0.252 Angle : 0.700 6.412 3378 Z= 0.393 Chirality : 0.060 0.246 444 Planarity : 0.003 0.011 420 Dihedral : 5.378 13.765 366 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.75 % Favored : 78.25 % Rotamer: Outliers : 6.50 % Allowed : 28.46 % Favored : 65.04 % 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: -4.44 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.018 0.005 PHE F 94 TYR 0.014 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.263 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 71 average time/residue: 0.8582 time to fit residues: 62.7368 Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0258 time to fit residues: 0.4032 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 0.0010 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2496 Z= 0.124 Angle : 0.572 5.004 3378 Z= 0.316 Chirality : 0.056 0.195 444 Planarity : 0.002 0.010 420 Dihedral : 4.318 14.682 366 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 2.85 % Allowed : 32.52 % Favored : 64.63 % 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: -3.98 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.015 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.271 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.8108 time to fit residues: 53.5099 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0258 time to fit residues: 0.3838 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.148334 restraints weight = 3274.147| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.28 r_work: 0.3968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2496 Z= 0.223 Angle : 0.675 6.092 3378 Z= 0.376 Chirality : 0.059 0.239 444 Planarity : 0.002 0.012 420 Dihedral : 5.183 13.722 366 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.06 % Favored : 79.94 % Rotamer: Outliers : 3.25 % Allowed : 31.30 % Favored : 65.45 % 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: -4.30 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 50 PHE 0.016 0.004 PHE F 94 TYR 0.014 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.21 seconds wall clock time: 29 minutes 29.17 seconds (1769.17 seconds total)