Starting phenix.real_space_refine on Thu Dec 7 23:17:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/12_2023/8cio_16683.pdb" } resolution = 3.5 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3485 2.51 5 N 965 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ASP 139": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5655 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "C" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "D" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "E" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Time building chain proxies: 3.56, per 1000 atoms: 0.63 Number of scatterers: 5655 At special positions: 0 Unit cell: (64.428, 64.428, 219.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1185 8.00 N 965 7.00 C 3485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 85 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 85 " distance=2.03 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP B 71 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 61 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN B 73 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 59 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLN A 34 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER B 62 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 36 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 170 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP A 71 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 61 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 73 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 59 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 36 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 62 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER A 102 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP C 71 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY C 61 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN C 73 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP C 59 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLN B 34 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER C 62 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 36 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 170 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER B 102 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER C 102 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP D 71 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 61 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN D 73 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 59 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 36 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 62 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 170 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER D 102 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 58 removed outlier: 3.684A pdb=" N GLY E 76 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER E 102 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 105 " --> pdb=" O SER E 102 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1905 1.34 - 1.46: 1123 1.46 - 1.57: 2682 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 5740 Sorted by residual: bond pdb=" CA THR E 77 " pdb=" CB THR E 77 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.22e-01 bond pdb=" CA THR C 77 " pdb=" CB THR C 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.85e-01 bond pdb=" CA THR B 77 " pdb=" CB THR B 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.56e-01 bond pdb=" CA THR A 77 " pdb=" CB THR A 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.49e-01 bond pdb=" CB ASP C 125 " pdb=" CG ASP C 125 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.43e-01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.49: 190 107.49 - 114.11: 3484 114.11 - 120.73: 1814 120.73 - 127.36: 2352 127.36 - 133.98: 50 Bond angle restraints: 7890 Sorted by residual: angle pdb=" CA THR D 77 " pdb=" CB THR D 77 " pdb=" CG2 THR D 77 " ideal model delta sigma weight residual 110.50 114.10 -3.60 1.70e+00 3.46e-01 4.48e+00 angle pdb=" CA THR A 77 " pdb=" CB THR A 77 " pdb=" CG2 THR A 77 " ideal model delta sigma weight residual 110.50 114.07 -3.57 1.70e+00 3.46e-01 4.41e+00 angle pdb=" CA THR B 77 " pdb=" CB THR B 77 " pdb=" CG2 THR B 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.40e+00 angle pdb=" CA THR C 77 " pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 angle pdb=" CA THR E 77 " pdb=" CB THR E 77 " pdb=" CG2 THR E 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.25: 2845 10.25 - 20.51: 305 20.51 - 30.76: 125 30.76 - 41.02: 45 41.02 - 51.27: 15 Dihedral angle restraints: 3335 sinusoidal: 1130 harmonic: 2205 Sorted by residual: dihedral pdb=" CA GLN B 133 " pdb=" CB GLN B 133 " pdb=" CG GLN B 133 " pdb=" CD GLN B 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.78 46.22 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN C 133 " pdb=" CB GLN C 133 " pdb=" CG GLN C 133 " pdb=" CD GLN C 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.79 46.21 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN A 133 " pdb=" CB GLN A 133 " pdb=" CG GLN A 133 " pdb=" CD GLN A 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.80 46.20 3 1.50e+01 4.44e-03 8.30e+00 ... (remaining 3332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.063: 204 0.063 - 0.095: 72 0.095 - 0.127: 84 0.127 - 0.159: 15 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CB THR D 77 " pdb=" CA THR D 77 " pdb=" OG1 THR D 77 " pdb=" CG2 THR D 77 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB THR A 77 " pdb=" CA THR A 77 " pdb=" OG1 THR A 77 " pdb=" CG2 THR A 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB THR B 77 " pdb=" CA THR B 77 " pdb=" OG1 THR B 77 " pdb=" CG2 THR B 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1002 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 151 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO B 152 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 152 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 151 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO E 152 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 151 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO C 152 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.014 5.00e-02 4.00e+02 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 2489 2.91 - 3.41: 5100 3.41 - 3.91: 8534 3.91 - 4.40: 9411 4.40 - 4.90: 16364 Nonbonded interactions: 41898 Sorted by model distance: nonbonded pdb=" O SER E 144 " pdb=" OG1 THR E 145 " model vdw 2.418 2.440 nonbonded pdb=" O SER C 144 " pdb=" OG1 THR C 145 " model vdw 2.418 2.440 nonbonded pdb=" O SER D 144 " pdb=" OG1 THR D 145 " model vdw 2.418 2.440 nonbonded pdb=" O SER B 144 " pdb=" OG1 THR B 145 " model vdw 2.418 2.440 nonbonded pdb=" O SER A 144 " pdb=" OG1 THR A 145 " model vdw 2.419 2.440 ... (remaining 41893 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.210 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.002 0.023 5740 Z= 0.156 Angle : 0.547 6.992 7890 Z= 0.284 Chirality : 0.048 0.159 1005 Planarity : 0.003 0.026 1015 Dihedral : 11.522 51.274 1930 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.60 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.41 (0.47), residues: 135 loop : -1.80 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 55 HIS 0.002 0.001 HIS D 100 PHE 0.004 0.001 PHE C 60 TYR 0.006 0.001 TYR B 120 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1095 time to fit residues: 18.9126 Evaluate side-chains 77 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 121 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5740 Z= 0.279 Angle : 0.602 8.953 7890 Z= 0.311 Chirality : 0.049 0.139 1005 Planarity : 0.003 0.026 1015 Dihedral : 4.318 18.590 835 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 2.06 % Allowed : 13.02 % Favored : 84.92 % 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: -1.73 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.24 (0.46), residues: 135 loop : -1.88 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 182 HIS 0.003 0.001 HIS D 63 PHE 0.012 0.002 PHE C 60 TYR 0.018 0.001 TYR D 107 ARG 0.002 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.661 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.1094 time to fit residues: 15.7754 Evaluate side-chains 82 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0540 time to fit residues: 1.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 150 ASN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5740 Z= 0.359 Angle : 0.635 10.438 7890 Z= 0.325 Chirality : 0.049 0.144 1005 Planarity : 0.004 0.027 1015 Dihedral : 4.876 28.953 835 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 3.17 % Allowed : 15.40 % Favored : 81.43 % 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: -1.91 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.94 (0.44), residues: 135 loop : -1.96 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 55 HIS 0.003 0.001 HIS D 63 PHE 0.010 0.002 PHE C 60 TYR 0.011 0.002 TYR D 123 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.646 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 0.1105 time to fit residues: 14.9911 Evaluate side-chains 77 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0615 time to fit residues: 1.7085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5740 Z= 0.287 Angle : 0.635 14.241 7890 Z= 0.312 Chirality : 0.049 0.142 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.675 24.356 835 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.34 % Favored : 88.03 % Rotamer: Outliers : 2.70 % Allowed : 18.57 % Favored : 78.73 % 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: -1.97 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.84 (0.44), residues: 135 loop : -1.99 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.003 0.001 HIS C 63 PHE 0.008 0.002 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.649 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 89 average time/residue: 0.1114 time to fit residues: 14.8739 Evaluate side-chains 73 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0507 time to fit residues: 1.6355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS E 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5740 Z= 0.228 Angle : 0.606 12.464 7890 Z= 0.298 Chirality : 0.049 0.237 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.451 25.630 835 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.70 % Favored : 88.66 % Rotamer: Outliers : 1.59 % Allowed : 20.63 % Favored : 77.78 % 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: -1.96 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.89 (0.44), residues: 135 loop : -1.99 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.003 0.001 HIS E 100 PHE 0.008 0.001 PHE C 60 TYR 0.011 0.001 TYR D 107 ARG 0.001 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.666 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 78 average time/residue: 0.1104 time to fit residues: 13.1356 Evaluate side-chains 67 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0547 time to fit residues: 1.0924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5740 Z= 0.198 Angle : 0.612 14.638 7890 Z= 0.296 Chirality : 0.051 0.327 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.216 24.939 835 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.83 % Favored : 88.54 % Rotamer: Outliers : 1.11 % Allowed : 22.06 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.97 (0.44), residues: 135 loop : -1.97 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 182 HIS 0.002 0.001 HIS D 63 PHE 0.006 0.001 PHE C 60 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.653 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 84 average time/residue: 0.1110 time to fit residues: 14.1801 Evaluate side-chains 70 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0568 time to fit residues: 1.0153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5740 Z= 0.226 Angle : 0.652 14.384 7890 Z= 0.310 Chirality : 0.051 0.287 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.249 25.523 835 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.59 % Favored : 87.77 % Rotamer: Outliers : 1.11 % Allowed : 22.70 % Favored : 76.19 % 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: -1.91 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.94 (0.45), residues: 135 loop : -1.96 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.002 0.001 HIS C 63 PHE 0.005 0.001 PHE C 60 TYR 0.009 0.001 TYR B 172 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.665 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.1184 time to fit residues: 13.3610 Evaluate side-chains 71 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0579 time to fit residues: 1.2758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 0.0040 chunk 69 optimal weight: 0.3980 chunk 63 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 5740 Z= 0.157 Angle : 0.620 12.852 7890 Z= 0.292 Chirality : 0.050 0.257 1005 Planarity : 0.003 0.026 1015 Dihedral : 3.775 18.010 835 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.30 % Favored : 90.06 % Rotamer: Outliers : 0.32 % Allowed : 22.70 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.10 (0.45), residues: 135 loop : -1.91 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 182 HIS 0.001 0.000 HIS B 63 PHE 0.003 0.001 PHE C 60 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.665 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.1142 time to fit residues: 13.8947 Evaluate side-chains 67 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5740 Z= 0.218 Angle : 0.674 15.642 7890 Z= 0.322 Chirality : 0.051 0.244 1005 Planarity : 0.003 0.028 1015 Dihedral : 3.893 19.352 835 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.96 % Favored : 88.41 % Rotamer: Outliers : 0.48 % Allowed : 23.97 % Favored : 75.56 % 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: -1.84 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.15 (0.46), residues: 135 loop : -1.95 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 182 HIS 0.002 0.001 HIS D 63 PHE 0.004 0.001 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.001 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.638 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.1152 time to fit residues: 12.1654 Evaluate side-chains 68 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0588 time to fit residues: 1.0153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 150 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5740 Z= 0.268 Angle : 0.691 14.916 7890 Z= 0.333 Chirality : 0.051 0.245 1005 Planarity : 0.003 0.029 1015 Dihedral : 4.388 25.114 835 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.64 % Rotamer: Outliers : 0.95 % Allowed : 23.65 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.07 (0.46), residues: 135 loop : -2.02 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.003 0.001 HIS E 100 PHE 0.006 0.001 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.002 0.000 ARG D 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.660 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.1145 time to fit residues: 12.6920 Evaluate side-chains 72 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0709 time to fit residues: 1.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.077421 restraints weight = 11473.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080077 restraints weight = 6213.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081904 restraints weight = 4056.540| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5740 Z= 0.260 Angle : 0.679 14.785 7890 Z= 0.328 Chirality : 0.051 0.240 1005 Planarity : 0.003 0.030 1015 Dihedral : 4.326 25.115 835 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.46 % Favored : 87.90 % Rotamer: Outliers : 0.32 % Allowed : 24.44 % Favored : 75.24 % 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: -1.97 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.06 (0.46), residues: 135 loop : -2.05 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.002 0.001 HIS A 100 PHE 0.005 0.001 PHE C 60 TYR 0.012 0.001 TYR B 172 ARG 0.002 0.000 ARG D 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1439.74 seconds wall clock time: 26 minutes 52.04 seconds (1612.04 seconds total)