Starting phenix.real_space_refine on Mon Sep 23 13:17:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/09_2024/6wkt_21708.cif" } resolution = 3.4 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 1884 2.51 5 N 556 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3152 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Restraints were copied for chains: C, B, D Time building chain proxies: 1.82, per 1000 atoms: 0.58 Number of scatterers: 3152 At special positions: 0 Unit cell: (79.056, 63.504, 55.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 620 8.00 N 556 7.00 C 1884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 399.7 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 58 Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 86 through 107 Processing helix chain 'C' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 62 through 82 Processing helix chain 'C' and resid 86 through 107 Processing helix chain 'D' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 58 Processing helix chain 'D' and resid 62 through 82 Processing helix chain 'D' and resid 86 through 107 296 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 884 1.34 - 1.46: 504 1.46 - 1.58: 1696 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 3192 Sorted by residual: bond pdb=" C ILE B 39 " pdb=" N ARG B 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE A 39 " pdb=" N ARG A 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE C 39 " pdb=" N ARG C 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C THR C 24 " pdb=" O THR C 24 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.08e+00 ... (remaining 3187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4116 1.62 - 3.23: 124 3.23 - 4.85: 24 4.85 - 6.47: 12 6.47 - 8.09: 8 Bond angle restraints: 4284 Sorted by residual: angle pdb=" C GLN D 32 " pdb=" N HIS D 33 " pdb=" CA HIS D 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN C 32 " pdb=" N HIS C 33 " pdb=" CA HIS C 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" O ILE D 39 " pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 121.90 118.01 3.89 1.04e+00 9.25e-01 1.40e+01 ... (remaining 4279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1820 17.75 - 35.49: 136 35.49 - 53.23: 24 53.23 - 70.97: 0 70.97 - 88.72: 8 Dihedral angle restraints: 1988 sinusoidal: 740 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 36 " pdb=" C SER A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER D 36 " pdb=" C SER D 36 " pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 280 0.034 - 0.068: 148 0.068 - 0.102: 36 0.102 - 0.136: 12 0.136 - 0.170: 4 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA THR D 24 " pdb=" N THR D 24 " pdb=" C THR D 24 " pdb=" CB THR D 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR C 24 " pdb=" N THR C 24 " pdb=" C THR C 24 " pdb=" CB THR C 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR B 24 " pdb=" N THR B 24 " pdb=" C THR B 24 " pdb=" CB THR B 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 477 not shown) Planarity restraints: 568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS B 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS B 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP B 85 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 84 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS D 84 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS D 84 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 85 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS C 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS C 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 85 " -0.016 2.00e-02 2.50e+03 ... (remaining 565 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1012 2.84 - 3.36: 3094 3.36 - 3.87: 5334 3.87 - 4.39: 5872 4.39 - 4.90: 10766 Nonbonded interactions: 26078 Sorted by model distance: nonbonded pdb=" O LYS D 54 " pdb=" OG1 THR D 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS B 54 " pdb=" OG1 THR B 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS A 54 " pdb=" OG1 THR A 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS C 54 " pdb=" OG1 THR C 58 " model vdw 2.329 3.040 nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 79 " model vdw 2.426 3.040 ... (remaining 26073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.050 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.004 0.037 3192 Z= 0.298 Angle : 0.808 8.085 4284 Z= 0.490 Chirality : 0.046 0.170 480 Planarity : 0.006 0.029 568 Dihedral : 13.975 88.716 1164 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.29), residues: 416 helix: -1.91 (0.19), residues: 368 sheet: None (None), residues: 0 loop : -3.11 (0.74), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 34 PHE 0.016 0.003 PHE A 23 TYR 0.006 0.002 TYR A 4 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.396 Fit side-chains REVERT: A 16 MET cc_start: 0.7205 (mtp) cc_final: 0.6914 (mtm) REVERT: A 80 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6400 (mm-30) REVERT: A 90 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8491 (mm-40) REVERT: B 16 MET cc_start: 0.7189 (mtp) cc_final: 0.6892 (mtm) REVERT: B 80 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6403 (mm-30) REVERT: B 90 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8495 (mm-40) REVERT: C 16 MET cc_start: 0.7198 (mtp) cc_final: 0.6894 (mtm) REVERT: C 80 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6407 (mm-30) REVERT: C 90 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8494 (mm-40) REVERT: D 16 MET cc_start: 0.7207 (mtp) cc_final: 0.6907 (mtm) REVERT: D 80 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6408 (mm-30) REVERT: D 90 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8496 (mm-40) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2408 time to fit residues: 20.7868 Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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: 0.7284 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.132 Angle : 0.470 4.485 4284 Z= 0.261 Chirality : 0.032 0.098 480 Planarity : 0.003 0.022 568 Dihedral : 4.059 12.818 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % 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: 0.67 (0.37), residues: 416 helix: 0.95 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -2.55 (0.66), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.006 0.001 PHE A 23 TYR 0.004 0.001 TYR A 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.367 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1562 time to fit residues: 15.8150 Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7278 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3192 Z= 0.159 Angle : 0.495 4.800 4284 Z= 0.277 Chirality : 0.033 0.106 480 Planarity : 0.003 0.017 568 Dihedral : 3.741 11.448 440 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % 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: 2.25 (0.38), residues: 416 helix: 1.97 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.72 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.010 0.002 PHE C 23 TYR 0.004 0.001 TYR B 4 ARG 0.005 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.395 Fit side-chains REVERT: A 59 ASP cc_start: 0.7659 (t0) cc_final: 0.7065 (t70) REVERT: B 59 ASP cc_start: 0.7653 (t0) cc_final: 0.7063 (t70) REVERT: C 59 ASP cc_start: 0.7668 (t0) cc_final: 0.7078 (t70) REVERT: D 59 ASP cc_start: 0.7666 (t0) cc_final: 0.7071 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1629 time to fit residues: 15.0073 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7228 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.130 Angle : 0.459 4.826 4284 Z= 0.259 Chirality : 0.032 0.099 480 Planarity : 0.003 0.016 568 Dihedral : 3.494 10.781 440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.38), residues: 416 helix: 2.62 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.34 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE B 23 TYR 0.004 0.001 TYR C 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.371 Fit side-chains REVERT: A 59 ASP cc_start: 0.7687 (t0) cc_final: 0.7179 (t70) REVERT: B 59 ASP cc_start: 0.7681 (t0) cc_final: 0.7177 (t70) REVERT: C 59 ASP cc_start: 0.7694 (t0) cc_final: 0.7186 (t70) REVERT: D 59 ASP cc_start: 0.7690 (t0) cc_final: 0.7182 (t70) REVERT: D 106 MET cc_start: 0.6532 (ppp) cc_final: 0.6331 (ptt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1539 time to fit residues: 14.9465 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.7293 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3192 Z= 0.206 Angle : 0.517 4.263 4284 Z= 0.285 Chirality : 0.035 0.107 480 Planarity : 0.003 0.014 568 Dihedral : 3.677 10.403 440 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % 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: 2.99 (0.38), residues: 416 helix: 2.45 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.31 (0.78), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.011 0.002 PHE D 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.379 Fit side-chains REVERT: A 59 ASP cc_start: 0.7817 (t0) cc_final: 0.7280 (t70) REVERT: A 75 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 59 ASP cc_start: 0.7807 (t0) cc_final: 0.7275 (t70) REVERT: B 75 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 59 ASP cc_start: 0.7824 (t0) cc_final: 0.7288 (t70) REVERT: C 75 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7434 (mm-30) REVERT: D 59 ASP cc_start: 0.7825 (t0) cc_final: 0.7301 (t70) REVERT: D 75 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7438 (mm-30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1667 time to fit residues: 15.6240 Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.7279 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3192 Z= 0.192 Angle : 0.517 4.406 4284 Z= 0.285 Chirality : 0.034 0.105 480 Planarity : 0.003 0.017 568 Dihedral : 3.674 10.417 440 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.38), residues: 416 helix: 2.66 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.11 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE D 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.364 Fit side-chains REVERT: A 59 ASP cc_start: 0.7855 (t0) cc_final: 0.7395 (t70) REVERT: B 59 ASP cc_start: 0.7850 (t0) cc_final: 0.7395 (t70) REVERT: C 59 ASP cc_start: 0.7862 (t0) cc_final: 0.7408 (t70) REVERT: D 59 ASP cc_start: 0.7844 (t0) cc_final: 0.7393 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1615 time to fit residues: 14.7277 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7248 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3192 Z= 0.162 Angle : 0.487 4.487 4284 Z= 0.273 Chirality : 0.034 0.105 480 Planarity : 0.003 0.021 568 Dihedral : 3.587 10.458 440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.38), residues: 416 helix: 2.90 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.96 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.010 0.002 PHE D 62 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.359 Fit side-chains REVERT: A 59 ASP cc_start: 0.7820 (t0) cc_final: 0.7393 (t70) REVERT: A 75 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 59 ASP cc_start: 0.7819 (t0) cc_final: 0.7390 (t70) REVERT: B 75 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7295 (mm-30) REVERT: C 59 ASP cc_start: 0.7826 (t0) cc_final: 0.7401 (t70) REVERT: C 75 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7201 (mm-30) REVERT: D 59 ASP cc_start: 0.7813 (t0) cc_final: 0.7422 (t70) REVERT: D 75 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7367 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1563 time to fit residues: 14.3148 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 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: 0.7211 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.142 Angle : 0.467 4.385 4284 Z= 0.262 Chirality : 0.033 0.105 480 Planarity : 0.003 0.023 568 Dihedral : 3.434 10.242 440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.86 % Allowed : 15.80 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.38), residues: 416 helix: 3.16 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.72 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE D 23 TYR 0.004 0.001 TYR D 4 ARG 0.007 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.357 Fit side-chains REVERT: A 59 ASP cc_start: 0.7824 (t0) cc_final: 0.7384 (t70) REVERT: A 75 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 59 ASP cc_start: 0.7820 (t0) cc_final: 0.7387 (t70) REVERT: B 75 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 59 ASP cc_start: 0.7829 (t0) cc_final: 0.7396 (t70) REVERT: C 75 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7243 (mm-30) REVERT: D 59 ASP cc_start: 0.7764 (t0) cc_final: 0.7394 (t70) REVERT: D 75 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7228 (mm-30) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 0.1588 time to fit residues: 14.5424 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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: 0.7205 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.131 Angle : 0.442 4.335 4284 Z= 0.251 Chirality : 0.032 0.106 480 Planarity : 0.003 0.022 568 Dihedral : 3.270 9.085 440 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.38), residues: 416 helix: 3.37 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.53 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 34 PHE 0.010 0.002 PHE D 23 TYR 0.003 0.001 TYR D 4 ARG 0.006 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.350 Fit side-chains REVERT: A 59 ASP cc_start: 0.7802 (t0) cc_final: 0.7380 (t70) REVERT: A 75 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 106 MET cc_start: 0.7159 (ppp) cc_final: 0.6400 (ppp) REVERT: B 59 ASP cc_start: 0.7801 (t0) cc_final: 0.7388 (t70) REVERT: B 75 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 106 MET cc_start: 0.7166 (ppp) cc_final: 0.6404 (ppp) REVERT: C 59 ASP cc_start: 0.7811 (t0) cc_final: 0.7391 (t70) REVERT: C 75 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7228 (mm-30) REVERT: C 106 MET cc_start: 0.7165 (ppp) cc_final: 0.6403 (ppp) REVERT: D 59 ASP cc_start: 0.7781 (t0) cc_final: 0.7401 (t70) REVERT: D 75 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7232 (mm-30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1624 time to fit residues: 14.6308 Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.7233 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3192 Z= 0.150 Angle : 0.454 4.206 4284 Z= 0.257 Chirality : 0.033 0.107 480 Planarity : 0.003 0.023 568 Dihedral : 3.260 8.358 440 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.37), residues: 416 helix: 3.32 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.51 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 34 PHE 0.010 0.002 PHE D 62 TYR 0.004 0.001 TYR D 4 ARG 0.007 0.001 ARG B 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.392 Fit side-chains REVERT: A 59 ASP cc_start: 0.7801 (t0) cc_final: 0.7405 (t70) REVERT: A 75 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 106 MET cc_start: 0.7128 (ppp) cc_final: 0.6450 (ppp) REVERT: B 59 ASP cc_start: 0.7809 (t0) cc_final: 0.7412 (t70) REVERT: B 75 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7262 (mm-30) REVERT: B 106 MET cc_start: 0.7142 (ppp) cc_final: 0.6460 (ppp) REVERT: C 59 ASP cc_start: 0.7811 (t0) cc_final: 0.7416 (t70) REVERT: C 75 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 106 MET cc_start: 0.7135 (ppp) cc_final: 0.6457 (ppp) REVERT: D 59 ASP cc_start: 0.7791 (t0) cc_final: 0.7407 (t70) REVERT: D 75 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7246 (mm-30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1713 time to fit residues: 15.4311 Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.232999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.202206 restraints weight = 3077.191| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.43 r_work: 0.3991 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3192 Z= 0.149 Angle : 0.453 4.218 4284 Z= 0.256 Chirality : 0.033 0.107 480 Planarity : 0.003 0.022 568 Dihedral : 3.260 8.233 440 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.37), residues: 416 helix: 3.38 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.47 (0.88), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 34 PHE 0.010 0.002 PHE B 23 TYR 0.004 0.001 TYR D 4 ARG 0.007 0.001 ARG D 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.59 seconds wall clock time: 20 minutes 8.70 seconds (1208.70 seconds total)