Starting phenix.real_space_refine (version: dev) on Fri Feb 17 05:44:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2023/6j6k_0690.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.012 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 Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3548 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.39, per 1000 atoms: 0.67 Number of scatterers: 3548 At special positions: 0 Unit cell: (70.551, 64.233, 66.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 704 8.00 N 620 7.00 C 2224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 567.6 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 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: 0 helices and 4 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 56 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 108 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 56 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 108 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 56 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 108 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.188A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 56 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D 108 " --> pdb=" O GLY D 126 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 408 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: 0.89 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.36: 584 1.36 - 1.42: 480 1.42 - 1.49: 623 1.49 - 1.55: 1377 Bond restraints: 3636 Sorted by residual: bond pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.31e+00 bond pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.24e+00 bond pdb=" N ALA C 50 " pdb=" CA ALA C 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" N ALA D 50 " pdb=" CA ALA D 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" C GLU C 44 " pdb=" N SER C 45 " ideal model delta sigma weight residual 1.332 1.352 -0.019 1.40e-02 5.10e+03 1.93e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 103.25 - 109.41: 510 109.41 - 115.56: 1768 115.56 - 121.72: 1699 121.72 - 127.87: 930 127.87 - 134.03: 69 Bond angle restraints: 4976 Sorted by residual: angle pdb=" C SER C 45 " pdb=" N ALA C 46 " pdb=" CA ALA C 46 " ideal model delta sigma weight residual 121.54 133.69 -12.15 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C SER D 45 " pdb=" N ALA D 46 " pdb=" CA ALA D 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER B 45 " pdb=" N ALA B 46 " pdb=" CA ALA B 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER A 45 " pdb=" N ALA A 46 " pdb=" CA ALA A 46 " ideal model delta sigma weight residual 121.54 133.67 -12.13 1.91e+00 2.74e-01 4.03e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 133.33 -11.36 1.80e+00 3.09e-01 3.98e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1860 16.16 - 32.33: 84 32.33 - 48.49: 28 48.49 - 64.65: 4 64.65 - 80.82: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual -180.00 -99.18 -80.82 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual -180.00 -99.21 -80.79 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual 180.00 -99.24 -80.76 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 356 0.042 - 0.084: 120 0.084 - 0.127: 52 0.127 - 0.169: 20 0.169 - 0.211: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA SER D 45 " pdb=" N SER D 45 " pdb=" C SER D 45 " pdb=" CB SER D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA SER A 45 " pdb=" N SER A 45 " pdb=" C SER A 45 " pdb=" CB SER A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 45 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C SER C 45 " -0.037 2.00e-02 2.50e+03 pdb=" O SER C 45 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 45 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C SER A 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER A 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 46 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 45 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C SER B 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER B 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA B 46 " -0.012 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1208 2.87 - 3.37: 2786 3.37 - 3.88: 5801 3.88 - 4.39: 6526 4.39 - 4.90: 12029 Nonbonded interactions: 28350 Sorted by model distance: nonbonded pdb=" O GLY D 34 " pdb=" OH TYR D 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY A 34 " pdb=" OH TYR A 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY B 34 " pdb=" OH TYR B 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY C 34 " pdb=" OH TYR C 60 " model vdw 2.358 2.440 nonbonded pdb=" NE1 TRP D 79 " pdb=" OG1 THR D 90 " model vdw 2.390 2.520 ... (remaining 28345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.130 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: 0.740 Check model and map are aligned: 0.050 Process input model: 14.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.005 0.037 3636 Z= 0.312 Angle : 1.220 12.150 4976 Z= 0.681 Chirality : 0.058 0.211 556 Planarity : 0.004 0.022 624 Dihedral : 12.694 80.818 1160 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 2.56 % Allowed : 6.84 % Favored : 90.60 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -4.75 (0.27), residues: 468 helix: None (None), residues: 0 sheet: -2.62 (0.25), residues: 264 loop : -3.78 (0.24), residues: 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.391 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 85 average time/residue: 0.1881 time to fit residues: 19.0861 Evaluate side-chains 46 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 118 ASN B 85 ASN C 82 ASN C 85 ASN D 82 ASN D 85 ASN D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3636 Z= 0.219 Angle : 0.790 7.066 4976 Z= 0.436 Chirality : 0.045 0.155 556 Planarity : 0.003 0.021 624 Dihedral : 8.264 62.054 512 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 1.71 % Allowed : 7.48 % Favored : 90.81 % Rotamer Outliers : 5.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.61 (0.31), residues: 468 helix: None (None), residues: 0 sheet: -1.79 (0.27), residues: 288 loop : -3.24 (0.27), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.412 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 76 average time/residue: 0.1206 time to fit residues: 12.9360 Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0568 time to fit residues: 1.8230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.0170 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.199 Angle : 0.730 6.395 4976 Z= 0.397 Chirality : 0.044 0.156 556 Planarity : 0.003 0.014 624 Dihedral : 7.364 52.764 512 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.56 % Favored : 92.74 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.15 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.45 (0.28), residues: 284 loop : -3.00 (0.27), residues: 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.387 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.0827 time to fit residues: 6.9412 Evaluate side-chains 51 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0362 time to fit residues: 0.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.0170 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.181 Angle : 0.664 5.883 4976 Z= 0.361 Chirality : 0.042 0.146 556 Planarity : 0.002 0.015 624 Dihedral : 6.765 46.357 512 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.98 % Favored : 92.31 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.08 (0.31), residues: 468 helix: None (None), residues: 0 sheet: -1.43 (0.28), residues: 280 loop : -2.88 (0.26), residues: 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.402 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.0831 time to fit residues: 7.2570 Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0375 time to fit residues: 0.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 0.0040 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 1.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3636 Z= 0.208 Angle : 0.665 5.151 4976 Z= 0.361 Chirality : 0.043 0.147 556 Planarity : 0.002 0.010 624 Dihedral : 6.410 39.271 512 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.77 % Favored : 92.52 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.79 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.19 (0.29), residues: 284 loop : -2.82 (0.26), residues: 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.392 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.0798 time to fit residues: 7.6054 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0364 time to fit residues: 0.7098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.204 Angle : 0.671 5.858 4976 Z= 0.362 Chirality : 0.043 0.141 556 Planarity : 0.002 0.009 624 Dihedral : 5.992 29.880 512 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.05 % Favored : 92.09 % Rotamer Outliers : 2.33 % 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: -2.57 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.01 (0.29), residues: 284 loop : -2.74 (0.27), residues: 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.390 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.0792 time to fit residues: 6.4509 Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0337 time to fit residues: 0.8719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3636 Z= 0.161 Angle : 0.658 5.964 4976 Z= 0.353 Chirality : 0.042 0.133 556 Planarity : 0.002 0.011 624 Dihedral : 5.494 21.070 512 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer Outliers : 1.45 % 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: -2.48 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -0.91 (0.29), residues: 276 loop : -2.71 (0.26), residues: 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.0759 time to fit residues: 6.7752 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0397 time to fit residues: 0.6826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 3636 Z= 0.361 Angle : 0.744 5.636 4976 Z= 0.401 Chirality : 0.045 0.134 556 Planarity : 0.003 0.015 624 Dihedral : 6.093 24.919 512 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.12 % Favored : 91.03 % Rotamer Outliers : 0.87 % 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: -2.30 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.77 (0.29), residues: 280 loop : -2.65 (0.27), residues: 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.385 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.0904 time to fit residues: 6.6325 Evaluate side-chains 50 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0547 time to fit residues: 0.5637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.0050 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.163 Angle : 0.666 5.983 4976 Z= 0.355 Chirality : 0.042 0.127 556 Planarity : 0.002 0.015 624 Dihedral : 5.510 25.953 512 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer Outliers : 0.58 % 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: -2.20 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -0.72 (0.29), residues: 276 loop : -2.54 (0.27), residues: 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.428 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.0807 time to fit residues: 6.3916 Evaluate side-chains 51 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.1980 chunk 21 optimal weight: 0.0040 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 87 HIS D 87 HIS D 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 3636 Z= 0.156 Angle : 0.666 6.682 4976 Z= 0.351 Chirality : 0.041 0.129 556 Planarity : 0.002 0.015 624 Dihedral : 5.017 25.578 512 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.49 % Favored : 94.66 % Rotamer Outliers : 0.87 % 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: -1.79 (0.34), residues: 468 helix: None (None), residues: 0 sheet: -0.41 (0.30), residues: 284 loop : -2.41 (0.29), residues: 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.393 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 66 average time/residue: 0.1454 time to fit residues: 12.0435 Evaluate side-chains 58 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129662 restraints weight = 4250.972| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.25 r_work: 0.3503 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 3636 Z= 0.313 Angle : 0.729 5.127 4976 Z= 0.390 Chirality : 0.044 0.128 556 Planarity : 0.003 0.017 624 Dihedral : 5.666 29.616 512 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.62 % Favored : 92.52 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.34), residues: 468 helix: None (None), residues: 0 sheet: -0.24 (0.31), residues: 280 loop : -2.51 (0.28), residues: 188 =============================================================================== Job complete usr+sys time: 1034.40 seconds wall clock time: 19 minutes 26.76 seconds (1166.76 seconds total)