Starting phenix.real_space_refine on Thu Dec 7 23:05:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/12_2023/7qv5_14167_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/12_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_14167/12_2023/7qv5_14167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/12_2023/7qv5_14167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/12_2023/7qv5_14167_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/12_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-1.21rc1-5172/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: 2.50, per 1000 atoms: 0.45 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: 4.35 Conformation dependent library (CDL) restraints added in 622.1 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: 0.72 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: 4.53 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: 2061 12.80 - 25.59: 117 25.59 - 38.39: 60 38.39 - 51.18: 30 51.18 - 63.98: 45 Dihedral angle restraints: 2313 sinusoidal: 1386 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 2310 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: 2.110 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: 0.090 Extract box with map and model: 7.490 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.520 Find NCS groups from input model: 0.300 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: 44.350 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG a 7 *********************** 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 : 0.473 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 4.8817 time to fit residues: 99.3629 Evaluate side-chains 8 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5584 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2538 Z= 0.095 Angle : 0.389 3.315 3384 Z= 0.195 Chirality : 0.061 0.129 468 Planarity : 0.001 0.006 405 Dihedral : 2.816 6.766 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.14 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: -2.22 (0.36), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 *********************** 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 10 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 3.9213 time to fit residues: 40.5053 Evaluate side-chains 6 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5518 ------------------------------------------------------------------------------- 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: 7.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.1944 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= 0.110 Angle : 0.357 2.616 3384 Z= 0.183 Chirality : 0.060 0.128 468 Planarity : 0.001 0.008 405 Dihedral : 2.979 6.819 342 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -2.13 (0.37), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 7 *********************** 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 10 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.514 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 5.1537 time to fit residues: 52.8145 Evaluate side-chains 9 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5674 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2538 Z= 0.154 Angle : 0.380 2.509 3384 Z= 0.195 Chirality : 0.059 0.129 468 Planarity : 0.002 0.008 405 Dihedral : 3.266 7.057 342 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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: -2.15 (0.38), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 7 *********************** 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 17 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.521 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 5.6648 time to fit residues: 97.9274 Evaluate side-chains 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5800 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8426 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2538 Z= 0.067 Angle : 0.321 2.325 3384 Z= 0.167 Chirality : 0.061 0.124 468 Planarity : 0.001 0.007 405 Dihedral : 2.543 5.744 342 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.86 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 *********************** 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 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 6.4516 time to fit residues: 98.3111 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5685 ------------------------------------------------------------------------------- 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: 8.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.2808 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= 0.125 Angle : 0.350 2.140 3384 Z= 0.182 Chirality : 0.059 0.127 468 Planarity : 0.001 0.007 405 Dihedral : 2.873 6.599 342 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -1.91 (0.40), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 *********************** 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 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 6.4620 time to fit residues: 98.3955 Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5742 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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: 0.8444 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= 0.108 Angle : 0.334 2.136 3384 Z= 0.174 Chirality : 0.060 0.125 468 Planarity : 0.001 0.007 405 Dihedral : 2.737 6.497 342 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.98 (0.40), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 7 *********************** 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 : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 6.5271 time to fit residues: 99.3917 Evaluate side-chains 13 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5614 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 2538 Z= 0.059 Angle : 0.307 2.095 3384 Z= 0.159 Chirality : 0.061 0.122 468 Planarity : 0.001 0.007 405 Dihedral : 2.301 5.618 342 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -1.72 (0.41), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 7 *********************** 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 19 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.596 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 19 average time/residue: 4.3505 time to fit residues: 84.3696 Evaluate side-chains 15 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1451 time to fit residues: 0.8002 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 2538 Z= 0.160 Angle : 0.369 1.998 3384 Z= 0.192 Chirality : 0.059 0.129 468 Planarity : 0.001 0.006 405 Dihedral : 2.952 6.901 342 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % 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: -2.00 (0.40), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 7 *********************** 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 : 0.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 6.4516 time to fit residues: 91.7626 Evaluate side-chains 14 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5601 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.3106 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= 0.110 Angle : 0.332 1.985 3384 Z= 0.173 Chirality : 0.060 0.123 468 Planarity : 0.001 0.005 405 Dihedral : 2.637 6.411 342 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % 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 (0.40), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 7 ********************** 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 13 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 6.9209 time to fit residues: 91.4722 Evaluate side-chains 13 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5709 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.131718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084276 restraints weight = 8211.757| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.10 r_work: 0.3223 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2538 Z= 0.076 Angle : 0.315 2.033 3384 Z= 0.164 Chirality : 0.061 0.124 468 Planarity : 0.001 0.005 405 Dihedral : 2.409 5.956 342 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.35 % Allowed : 8.68 % Favored : 90.97 % 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: -1.71 (0.41), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.59 seconds wall clock time: 50 minutes 58.72 seconds (3058.72 seconds total)