Starting phenix.real_space_refine on Thu Dec 7 15:48:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppo_17806/12_2023/8ppo_17806.pdb" } resolution = 2.0 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= 0.001 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 1088 2.51 5 N 272 2.21 5 O 336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 1696 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "K" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "L" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "M" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 1.23, per 1000 atoms: 0.73 Number of scatterers: 1696 At special positions: 0 Unit cell: (69.1961, 40.2914, 55.1817, 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 336 8.00 N 272 7.00 C 1088 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: 0.72 Conformation dependent library (CDL) restraints added in 395.4 milliseconds 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'I' and resid 306 through 310 Processing sheet with id=AA4, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.097A pdb=" N ASP L 314 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP N 314 " --> pdb=" O LEU O 315 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 288 1.29 - 1.36: 240 1.36 - 1.42: 128 1.42 - 1.48: 272 1.48 - 1.54: 784 Bond restraints: 1712 Sorted by residual: bond pdb=" N GLY C 302 " pdb=" CA GLY C 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.65e+00 bond pdb=" N GLY G 302 " pdb=" CA GLY G 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.57e+00 bond pdb=" N GLY O 302 " pdb=" CA GLY O 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.47e+00 bond pdb=" N GLY K 302 " pdb=" CA GLY K 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.44e+00 bond pdb=" N GLY D 302 " pdb=" CA GLY D 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.41e+00 ... (remaining 1707 not shown) Histogram of bond angle deviations from ideal: 103.62 - 108.76: 110 108.76 - 113.89: 906 113.89 - 119.02: 395 119.02 - 124.15: 850 124.15 - 129.28: 43 Bond angle restraints: 2304 Sorted by residual: angle pdb=" N TYR D 310 " pdb=" CA TYR D 310 " pdb=" C TYR D 310 " ideal model delta sigma weight residual 107.69 119.51 -11.82 2.01e+00 2.48e-01 3.46e+01 angle pdb=" N TYR L 310 " pdb=" CA TYR L 310 " pdb=" C TYR L 310 " ideal model delta sigma weight residual 108.02 118.24 -10.22 1.75e+00 3.27e-01 3.41e+01 angle pdb=" C TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta sigma weight residual 110.74 115.91 -5.17 1.61e+00 3.86e-01 1.03e+01 angle pdb=" CA TYR I 310 " pdb=" CB TYR I 310 " pdb=" CG TYR I 310 " ideal model delta sigma weight residual 113.90 118.69 -4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" CA TYR N 310 " pdb=" CB TYR N 310 " pdb=" CG TYR N 310 " ideal model delta sigma weight residual 113.90 118.59 -4.69 1.80e+00 3.09e-01 6.79e+00 ... (remaining 2299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.67: 871 10.67 - 21.33: 73 21.33 - 32.00: 16 32.00 - 42.66: 1 42.66 - 53.33: 31 Dihedral angle restraints: 992 sinusoidal: 368 harmonic: 624 Sorted by residual: dihedral pdb=" C TYR L 310 " pdb=" N TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta harmonic sigma weight residual -122.60 -134.88 12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C TYR D 310 " pdb=" N TYR D 310 " pdb=" CA TYR D 310 " pdb=" CB TYR D 310 " ideal model delta harmonic sigma weight residual -122.60 -133.55 10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" N TYR L 310 " pdb=" C TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta harmonic sigma weight residual 122.80 131.75 -8.95 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 989 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.095: 230 0.095 - 0.190: 40 0.190 - 0.284: 0 0.284 - 0.378: 0 0.378 - 0.473: 2 Chirality restraints: 272 Sorted by residual: chirality pdb=" CA TYR L 310 " pdb=" N TYR L 310 " pdb=" C TYR L 310 " pdb=" CB TYR L 310 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA TYR D 310 " pdb=" N TYR D 310 " pdb=" C TYR D 310 " pdb=" CB TYR D 310 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA VAL H 309 " pdb=" N VAL H 309 " pdb=" C VAL H 309 " pdb=" CB VAL H 309 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 269 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 310 " -0.024 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR N 310 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR N 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR N 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR N 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR N 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR N 310 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR N 310 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.019 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR F 310 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.033 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.023 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR G 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.025 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 1084 3.08 - 3.54: 1371 3.54 - 3.99: 2495 3.99 - 4.45: 2858 4.45 - 4.90: 4710 Nonbonded interactions: 12518 Sorted by model distance: nonbonded pdb=" OH TYR A 310 " pdb=" O GLY I 303 " model vdw 2.625 2.440 nonbonded pdb=" OH TYR H 310 " pdb=" O GLY P 303 " model vdw 2.647 2.440 nonbonded pdb=" O GLY B 303 " pdb=" OH TYR I 310 " model vdw 2.683 2.440 nonbonded pdb=" O GLY C 303 " pdb=" OH TYR J 310 " model vdw 2.684 2.440 nonbonded pdb=" OH TYR E 310 " pdb=" O GLY M 303 " model vdw 2.694 2.440 ... (remaining 12513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 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: 23.810 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.150 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.008 0.044 1712 Z= 0.506 Angle : 1.197 11.822 2304 Z= 0.664 Chirality : 0.074 0.473 272 Planarity : 0.006 0.027 288 Dihedral : 13.412 53.329 608 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.52 % 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: 0.71 (0.55), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.55 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.046 0.012 TYR N 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 1.3433 time to fit residues: 43.7926 Evaluate side-chains 30 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1712 Z= 0.247 Angle : 0.564 3.400 2304 Z= 0.294 Chirality : 0.057 0.135 272 Planarity : 0.004 0.019 288 Dihedral : 4.984 14.354 240 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: 1.38 (0.59), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.06 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR L 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.2871 time to fit residues: 49.7650 Evaluate side-chains 36 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN H 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1712 Z= 0.223 Angle : 0.518 3.345 2304 Z= 0.270 Chirality : 0.057 0.133 272 Planarity : 0.003 0.016 288 Dihedral : 4.878 13.702 240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 6.77 % Favored : 92.71 % 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: 1.41 (0.62), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.09 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.213 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 1.3930 time to fit residues: 49.5722 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.2643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 12 optimal weight: 0.5980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.237 Angle : 0.510 3.473 2304 Z= 0.264 Chirality : 0.057 0.134 272 Planarity : 0.003 0.015 288 Dihedral : 4.859 13.706 240 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 5.21 % Favored : 93.75 % 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: 1.36 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.05 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.208 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 1.3618 time to fit residues: 51.2412 Evaluate side-chains 36 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1712 Z= 0.188 Angle : 0.484 3.410 2304 Z= 0.250 Chirality : 0.057 0.133 272 Planarity : 0.003 0.014 288 Dihedral : 4.678 13.310 240 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 5.21 % Favored : 93.75 % 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: 1.32 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.02 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.259 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 1.4628 time to fit residues: 56.5901 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.248 Angle : 0.511 3.411 2304 Z= 0.265 Chirality : 0.056 0.132 272 Planarity : 0.003 0.013 288 Dihedral : 4.828 13.450 240 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.77 % Favored : 92.19 % 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: 1.27 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.98 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR P 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.221 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 1.4145 time to fit residues: 51.7186 Evaluate side-chains 36 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.254 Angle : 0.511 3.332 2304 Z= 0.265 Chirality : 0.057 0.132 272 Planarity : 0.003 0.014 288 Dihedral : 4.794 13.476 240 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.77 % Favored : 92.19 % 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: 1.25 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.96 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR P 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.195 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.5688 time to fit residues: 55.7297 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.258 Angle : 0.513 3.340 2304 Z= 0.266 Chirality : 0.057 0.132 272 Planarity : 0.002 0.013 288 Dihedral : 4.826 13.481 240 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.77 % Favored : 92.19 % 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: 1.22 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.94 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR P 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.208 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.5142 time to fit residues: 53.8364 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.218 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.254 Angle : 0.510 3.369 2304 Z= 0.264 Chirality : 0.057 0.132 272 Planarity : 0.002 0.012 288 Dihedral : 4.816 13.444 240 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.77 % Favored : 92.19 % 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: 1.20 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.93 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR P 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.217 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.5461 time to fit residues: 54.9274 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1712 Z= 0.188 Angle : 0.481 3.272 2304 Z= 0.249 Chirality : 0.057 0.133 272 Planarity : 0.002 0.013 288 Dihedral : 4.642 13.394 240 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 7.29 % Favored : 91.67 % 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: 1.24 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.96 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.174 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.5875 time to fit residues: 56.3937 Evaluate side-chains 35 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.122549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076667 restraints weight = 1400.596| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.32 r_work: 0.3248 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.239 Angle : 0.504 3.280 2304 Z= 0.261 Chirality : 0.057 0.132 272 Planarity : 0.002 0.013 288 Dihedral : 4.775 13.493 240 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 7.29 % Favored : 91.67 % 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: 1.18 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.91 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR P 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.16 seconds wall clock time: 36 minutes 39.20 seconds (2199.20 seconds total)