Starting phenix.real_space_refine on Mon Nov 13 21:47:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/11_2023/7qv5_14167_trim_updated.pdb" } resolution = 3.0 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= 0.005 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 C 1638 2.51 5 N 495 2.21 5 O 432 1.98 5 H 2997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "D ASP 4": "OD1" <-> "OD2" Residue "G ASP 4": "OD1" <-> "OD2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "P ASP 4": "OD1" <-> "OD2" Residue "S ASP 4": "OD1" <-> "OD2" Residue "V ASP 4": "OD1" <-> "OD2" Residue "Y ASP 4": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 5562 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "D" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "E" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "H" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "K" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "L" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "N" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "Q" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "S" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "T" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "V" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "W" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Chain: "Y" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 272 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "Z" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 13} Chain: "a" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Time building chain proxies: 2.32, per 1000 atoms: 0.42 Number of scatterers: 5562 At special positions: 0 Unit cell: (114.75, 123.25, 29.75, 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) O 432 8.00 N 495 7.00 C 1638 6.00 H 2997 1.00 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: 4.06 Conformation dependent library (CDL) restraints added in 587.5 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2997 0.98 - 1.12: 0 1.12 - 1.26: 414 1.26 - 1.40: 432 1.40 - 1.54: 1692 Bond restraints: 5535 Sorted by residual: bond pdb=" C VAL T 17 " pdb=" N NH2 T 18 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" C VAL H 17 " pdb=" N NH2 H 18 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" C VAL E 17 " pdb=" N NH2 E 18 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" C VAL K 17 " pdb=" N NH2 K 18 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" C VAL B 17 " pdb=" N NH2 B 18 " ideal model delta sigma weight residual 2.329 1.325 1.004 1.40e-02 5.10e+03 5.15e+03 ... (remaining 5530 not shown) Histogram of bond angle deviations from ideal: 105.91 - 109.75: 4710 109.75 - 113.60: 3063 113.60 - 117.44: 615 117.44 - 121.28: 711 121.28 - 125.12: 1062 Bond angle restraints: 10161 Sorted by residual: angle pdb=" N VAL F 2 " pdb=" CA VAL F 2 " pdb=" C VAL F 2 " ideal model delta sigma weight residual 109.34 106.05 3.29 2.08e+00 2.31e-01 2.49e+00 angle pdb=" N VAL R 2 " pdb=" CA VAL R 2 " pdb=" C VAL R 2 " ideal model delta sigma weight residual 109.34 106.07 3.27 2.08e+00 2.31e-01 2.47e+00 angle pdb=" N VAL a 2 " pdb=" CA VAL a 2 " pdb=" C VAL a 2 " ideal model delta sigma weight residual 109.34 106.07 3.27 2.08e+00 2.31e-01 2.47e+00 angle pdb=" N VAL I 2 " pdb=" CA VAL I 2 " pdb=" C VAL I 2 " ideal model delta sigma weight residual 109.34 106.08 3.26 2.08e+00 2.31e-01 2.46e+00 angle pdb=" N VAL U 2 " pdb=" CA VAL U 2 " pdb=" C VAL U 2 " ideal model delta sigma weight residual 109.34 106.08 3.26 2.08e+00 2.31e-01 2.45e+00 ... (remaining 10156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.80: 1782 12.80 - 25.59: 117 25.59 - 38.39: 60 38.39 - 51.18: 30 51.18 - 63.98: 45 Dihedral angle restraints: 2034 sinusoidal: 1107 harmonic: 927 Sorted by residual: dihedral pdb=" CA LEU S 5 " pdb=" CB LEU S 5 " pdb=" CG LEU S 5 " pdb=" CD1 LEU S 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.53 34.47 3 1.50e+01 4.44e-03 5.84e+00 dihedral pdb=" CA LEU G 5 " pdb=" CB LEU G 5 " pdb=" CG LEU G 5 " pdb=" CD1 LEU G 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.54 34.46 3 1.50e+01 4.44e-03 5.84e+00 dihedral pdb=" CA LEU J 5 " pdb=" CB LEU J 5 " pdb=" CG LEU J 5 " pdb=" CD1 LEU J 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.55 34.45 3 1.50e+01 4.44e-03 5.84e+00 ... (remaining 2031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 166 0.024 - 0.049: 121 0.049 - 0.073: 46 0.073 - 0.097: 111 0.097 - 0.121: 24 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILE H 6 " pdb=" N ILE H 6 " pdb=" C ILE H 6 " pdb=" CB ILE H 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE T 6 " pdb=" N ILE T 6 " pdb=" C ILE T 6 " pdb=" CB ILE T 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE B 6 " pdb=" N ILE B 6 " pdb=" C ILE B 6 " pdb=" CB ILE B 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 465 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 1 " 0.002 2.00e-02 2.50e+03 3.83e-03 1.47e-01 pdb=" N VAL R 2 " -0.007 2.00e-02 2.50e+03 pdb=" CA VAL R 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL R 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 1 " 0.002 2.00e-02 2.50e+03 3.75e-03 1.41e-01 pdb=" N VAL I 2 " -0.006 2.00e-02 2.50e+03 pdb=" CA VAL I 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL I 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY a 1 " 0.002 2.00e-02 2.50e+03 3.68e-03 1.35e-01 pdb=" N VAL a 2 " -0.006 2.00e-02 2.50e+03 pdb=" CA VAL a 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL a 2 " 0.003 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.41: 2863 2.41 - 2.90: 12430 2.90 - 3.40: 10148 3.40 - 3.90: 14712 3.90 - 4.40: 19153 Nonbonded interactions: 59306 Sorted by model distance: nonbonded pdb=" HD2 ARG G 7 " pdb="HH11 ARG G 7 " model vdw 1.908 2.270 nonbonded pdb=" HD2 ARG P 7 " pdb="HH11 ARG P 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG Y 7 " pdb="HH11 ARG Y 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG J 7 " pdb="HH11 ARG J 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG A 7 " pdb="HH11 ARG A 7 " model vdw 1.909 2.270 ... (remaining 59301 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 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' } 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: 3.040 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: 0.080 Extract box with map and model: 7.710 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.085 1.005 2538 Z= 6.050 Angle : 0.440 3.285 3384 Z= 0.230 Chirality : 0.057 0.121 468 Planarity : 0.002 0.008 405 Dihedral : 9.436 34.465 954 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -2.64 (0.35), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 4.7976 time to fit residues: 97.5902 Evaluate side-chains 8 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2538 Z= 0.092 Angle : 0.387 3.324 3384 Z= 0.194 Chirality : 0.060 0.127 468 Planarity : 0.001 0.005 405 Dihedral : 2.833 6.792 342 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.36), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.374 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 3.5196 time to fit residues: 32.7359 Evaluate side-chains 6 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8394 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2538 Z= 0.072 Angle : 0.325 2.588 3384 Z= 0.168 Chirality : 0.061 0.125 468 Planarity : 0.001 0.006 405 Dihedral : 2.637 6.497 342 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.87 (0.38), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.477 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 4.1732 time to fit residues: 38.7042 Evaluate side-chains 7 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 2538 Z= 0.137 Angle : 0.367 2.381 3384 Z= 0.189 Chirality : 0.059 0.130 468 Planarity : 0.002 0.009 405 Dihedral : 3.119 6.796 342 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.95 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.477 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 5.1816 time to fit residues: 79.1726 Evaluate side-chains 12 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.068 Angle : 0.318 2.227 3384 Z= 0.165 Chirality : 0.061 0.125 468 Planarity : 0.001 0.007 405 Dihedral : 2.582 5.740 342 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 7.29 % 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: -1.70 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.484 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 5.5536 time to fit residues: 79.1603 Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2538 Z= 0.072 Angle : 0.316 2.082 3384 Z= 0.165 Chirality : 0.061 0.125 468 Planarity : 0.001 0.008 405 Dihedral : 2.523 5.613 342 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -1.51 (0.41), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.31), residues: 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.505 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 5.5029 time to fit residues: 78.4570 Evaluate side-chains 12 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.8403 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2538 Z= 0.056 Angle : 0.301 1.997 3384 Z= 0.156 Chirality : 0.061 0.124 468 Planarity : 0.001 0.007 405 Dihedral : 2.269 5.146 342 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 7.29 % 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: -1.34 (0.41), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 4.0937 time to fit residues: 62.8077 Evaluate side-chains 10 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2538 Z= 0.066 Angle : 0.306 1.917 3384 Z= 0.158 Chirality : 0.061 0.124 468 Planarity : 0.001 0.006 405 Dihedral : 2.335 5.334 342 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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: -1.29 (0.42), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.32), residues: 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.518 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 5.6456 time to fit residues: 57.7208 Evaluate side-chains 10 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2538 Z= 0.069 Angle : 0.307 1.910 3384 Z= 0.159 Chirality : 0.061 0.124 468 Planarity : 0.001 0.006 405 Dihedral : 2.348 5.504 342 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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: -1.23 (0.42), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.506 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 5.5885 time to fit residues: 79.6750 Evaluate side-chains 13 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2538 Z= 0.076 Angle : 0.316 2.097 3384 Z= 0.162 Chirality : 0.061 0.124 468 Planarity : 0.001 0.006 405 Dihedral : 2.381 5.676 342 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % 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 (0.41), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 5.4573 time to fit residues: 77.8971 Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7102 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.132446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084902 restraints weight = 8149.473| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.15 r_work: 0.3270 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2538 Z= 0.060 Angle : 0.309 2.047 3384 Z= 0.159 Chirality : 0.061 0.123 468 Planarity : 0.001 0.006 405 Dihedral : 2.286 5.481 342 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % 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: -1.05 (0.42), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.03 seconds wall clock time: 50 minutes 2.41 seconds (3002.41 seconds total)