Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:01:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/04_2023/8a02_15045.pdb" } resolution = 3.2 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= 0.017 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 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "E" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "D" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.51, per 1000 atoms: 0.64 Number of scatterers: 5511 At special positions: 0 Unit cell: (94.24, 96.72, 63.24, 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 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.82 Conformation dependent library (CDL) restraints added in 911.9 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 19 sheets defined 9.5% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.922A pdb=" N LEU F 35 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 178 through 187 removed outlier: 3.565A pdb=" N ARG F 187 " --> pdb=" O GLN F 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 60 through 66 Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 178 through 187 Processing sheet with id=AA1, first strand: chain 'F' and resid 2 through 7 removed outlier: 5.892A pdb=" N LYS F 2 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY F 119 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 4 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 23 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 15 through 17 removed outlier: 7.190A pdb=" N ILE F 42 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASN F 56 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE F 44 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU F 54 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ARG F 46 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL F 52 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 93 through 94 removed outlier: 5.967A pdb=" N SER F 93 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 128 through 137 removed outlier: 5.517A pdb=" N ASN F 230 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU F 153 " --> pdb=" O ARG F 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 143 through 146 removed outlier: 6.601A pdb=" N GLN F 168 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 219 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER F 166 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE F 221 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP F 164 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS F 223 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 162 " --> pdb=" O LYS F 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 7 removed outlier: 5.694A pdb=" N LYS E 2 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 119 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 4 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 23 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 15 through 17 removed outlier: 3.695A pdb=" N SER E 101 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE E 40 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN E 56 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 42 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.751A pdb=" N SER E 93 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 137 removed outlier: 5.192A pdb=" N ASN E 230 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU E 153 " --> pdb=" O ARG E 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 146 removed outlier: 3.937A pdb=" N LEU E 165 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 7 removed outlier: 6.654A pdb=" N LEU D 117 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR D 5 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 115 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 27 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.657A pdb=" N SER D 93 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 128 through 137 removed outlier: 5.268A pdb=" N ASN D 230 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 153 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 143 through 146 removed outlier: 3.601A pdb=" N GLY D 218 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 194 through 195 224 hydrogen bonds defined for protein. 594 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: 1.58 Time building geometry restraints manager: 2.01 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: 1818 1.34 - 1.46: 866 1.46 - 1.57: 2863 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" N GLY F 49 " pdb=" CA GLY F 49 " ideal model delta sigma weight residual 1.449 1.465 -0.015 1.45e-02 4.76e+03 1.14e+00 bond pdb=" CG LEU F 117 " pdb=" CD2 LEU F 117 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.89e-01 bond pdb=" N GLY E 119 " pdb=" CA GLY E 119 " ideal model delta sigma weight residual 1.449 1.457 -0.008 1.14e-02 7.69e+03 4.54e-01 bond pdb=" CG LEU F 26 " pdb=" CD2 LEU F 26 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.08e-01 bond pdb=" CG1 ILE E 155 " pdb=" CD1 ILE E 155 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.82e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 100.60 - 106.72: 69 106.72 - 112.85: 3138 112.85 - 118.97: 1514 118.97 - 125.09: 2806 125.09 - 131.22: 21 Bond angle restraints: 7548 Sorted by residual: angle pdb=" C LEU F 26 " pdb=" N SER F 27 " pdb=" CA SER F 27 " ideal model delta sigma weight residual 122.73 119.59 3.14 1.62e+00 3.81e-01 3.77e+00 angle pdb=" C GLY F 47 " pdb=" N ASN F 48 " pdb=" CA ASN F 48 " ideal model delta sigma weight residual 123.25 120.28 2.97 1.69e+00 3.50e-01 3.09e+00 angle pdb=" C GLY F 49 " pdb=" N SER F 50 " pdb=" CA SER F 50 " ideal model delta sigma weight residual 121.54 124.68 -3.14 1.91e+00 2.74e-01 2.71e+00 angle pdb=" CA LEU F 153 " pdb=" CB LEU F 153 " pdb=" CG LEU F 153 " ideal model delta sigma weight residual 116.30 122.04 -5.74 3.50e+00 8.16e-02 2.69e+00 angle pdb=" C ILE F 42 " pdb=" N TYR F 43 " pdb=" CA TYR F 43 " ideal model delta sigma weight residual 122.11 119.58 2.53 1.59e+00 3.96e-01 2.54e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3090 17.88 - 35.76: 259 35.76 - 53.64: 52 53.64 - 71.52: 11 71.52 - 89.40: 8 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA ASP F 198 " pdb=" CB ASP F 198 " pdb=" CG ASP F 198 " pdb=" OD1 ASP F 198 " ideal model delta sinusoidal sigma weight residual -30.00 -88.02 58.02 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU D 45 " pdb=" CG GLU D 45 " pdb=" CD GLU D 45 " pdb=" OE1 GLU D 45 " ideal model delta sinusoidal sigma weight residual 0.00 -84.79 84.79 1 3.00e+01 1.11e-03 9.70e+00 dihedral pdb=" CG ARG E 114 " pdb=" CD ARG E 114 " pdb=" NE ARG E 114 " pdb=" CZ ARG E 114 " ideal model delta sinusoidal sigma weight residual -90.00 -131.38 41.38 2 1.50e+01 4.44e-03 9.32e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 579 0.031 - 0.063: 204 0.063 - 0.094: 60 0.094 - 0.125: 82 0.125 - 0.156: 11 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE F 42 " pdb=" N ILE F 42 " pdb=" C ILE F 42 " pdb=" CB ILE F 42 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE F 83 " pdb=" N ILE F 83 " pdb=" C ILE F 83 " pdb=" CB ILE F 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE E 42 " pdb=" N ILE E 42 " pdb=" C ILE E 42 " pdb=" CB ILE E 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 178 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO E 179 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 178 " -0.004 2.00e-02 2.50e+03 8.06e-03 6.50e-01 pdb=" C LEU E 178 " 0.014 2.00e-02 2.50e+03 pdb=" O LEU E 178 " -0.005 2.00e-02 2.50e+03 pdb=" N PRO E 179 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 122 " 0.013 5.00e-02 4.00e+02 1.99e-02 6.31e-01 pdb=" N PRO F 123 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO F 123 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 123 " 0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1162 2.79 - 3.32: 4453 3.32 - 3.85: 8367 3.85 - 4.37: 9799 4.37 - 4.90: 18508 Nonbonded interactions: 42289 Sorted by model distance: nonbonded pdb=" NZ LYS E 2 " pdb=" OG1 THR E 5 " model vdw 2.264 2.520 nonbonded pdb=" OD1 ASN F 80 " pdb=" NH2 ARG F 114 " model vdw 2.395 2.520 nonbonded pdb=" N GLY D 22 " pdb=" O ILE D 120 " model vdw 2.406 2.520 nonbonded pdb=" O GLU D 140 " pdb=" NE2 GLN D 225 " model vdw 2.409 2.520 nonbonded pdb=" OG SER F 76 " pdb=" N ASP F 77 " model vdw 2.443 2.520 ... (remaining 42284 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 'D' selection = chain 'E' selection = chain 'F' } 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: 0.350 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: 2.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.003 0.024 5571 Z= 0.167 Angle : 0.469 5.739 7548 Z= 0.257 Chirality : 0.047 0.156 936 Planarity : 0.003 0.026 960 Dihedral : 14.611 89.400 2064 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 711 helix: 0.95 (0.67), residues: 60 sheet: 0.70 (0.30), residues: 300 loop : -0.53 (0.33), residues: 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.697 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1609 time to fit residues: 23.7660 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 5571 Z= 0.441 Angle : 0.626 5.968 7548 Z= 0.334 Chirality : 0.052 0.169 936 Planarity : 0.004 0.033 960 Dihedral : 4.617 17.614 750 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer Outliers : 2.54 % 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: -0.31 (0.31), residues: 711 helix: 0.31 (0.64), residues: 60 sheet: 0.37 (0.30), residues: 300 loop : -0.76 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.714 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.1564 time to fit residues: 22.0383 Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0547 time to fit residues: 2.2887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5571 Z= 0.281 Angle : 0.519 5.585 7548 Z= 0.283 Chirality : 0.049 0.159 936 Planarity : 0.003 0.032 960 Dihedral : 4.366 15.012 750 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.97 % Favored : 97.89 % Rotamer Outliers : 0.95 % 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: -0.30 (0.31), residues: 711 helix: 0.31 (0.65), residues: 60 sheet: 0.45 (0.30), residues: 297 loop : -0.83 (0.32), residues: 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.705 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.1668 time to fit residues: 20.2817 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0578 time to fit residues: 1.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.0040 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 5571 Z= 0.131 Angle : 0.425 4.729 7548 Z= 0.235 Chirality : 0.046 0.145 936 Planarity : 0.003 0.028 960 Dihedral : 3.867 14.407 750 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.43 % 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: -0.03 (0.32), residues: 711 helix: 0.67 (0.67), residues: 60 sheet: 0.60 (0.30), residues: 297 loop : -0.65 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.662 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.1703 time to fit residues: 21.8329 Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1146 time to fit residues: 1.8284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5571 Z= 0.235 Angle : 0.481 5.254 7548 Z= 0.263 Chirality : 0.047 0.153 936 Planarity : 0.003 0.029 960 Dihedral : 4.094 15.772 750 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 711 helix: 0.51 (0.66), residues: 60 sheet: 0.60 (0.30), residues: 297 loop : -0.69 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.724 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1432 time to fit residues: 17.9998 Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0553 time to fit residues: 1.8245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5571 Z= 0.216 Angle : 0.474 5.467 7548 Z= 0.260 Chirality : 0.047 0.157 936 Planarity : 0.003 0.029 960 Dihedral : 4.077 15.410 750 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.27 % 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: -0.06 (0.32), residues: 711 helix: 0.48 (0.65), residues: 60 sheet: 0.62 (0.30), residues: 297 loop : -0.66 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.707 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 85 average time/residue: 0.1605 time to fit residues: 18.5096 Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0546 time to fit residues: 1.3452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 5571 Z= 0.311 Angle : 0.529 5.753 7548 Z= 0.288 Chirality : 0.049 0.179 936 Planarity : 0.003 0.031 960 Dihedral : 4.334 15.706 750 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer Outliers : 1.43 % 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: -0.21 (0.31), residues: 711 helix: 0.23 (0.64), residues: 60 sheet: 0.52 (0.30), residues: 297 loop : -0.74 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.722 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.1725 time to fit residues: 19.4049 Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0597 time to fit residues: 1.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5571 Z= 0.129 Angle : 0.428 4.960 7548 Z= 0.237 Chirality : 0.046 0.144 936 Planarity : 0.003 0.030 960 Dihedral : 3.826 15.553 750 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.32), residues: 711 helix: 0.59 (0.66), residues: 60 sheet: 0.63 (0.30), residues: 297 loop : -0.60 (0.34), residues: 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.805 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.1575 time to fit residues: 18.7677 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0676 time to fit residues: 1.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5571 Z= 0.282 Angle : 0.508 5.646 7548 Z= 0.278 Chirality : 0.048 0.160 936 Planarity : 0.003 0.031 960 Dihedral : 4.186 15.736 750 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 1.59 % 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: -0.12 (0.32), residues: 711 helix: 0.34 (0.64), residues: 60 sheet: 0.55 (0.30), residues: 297 loop : -0.66 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.693 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1611 time to fit residues: 18.2912 Evaluate side-chains 80 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0595 time to fit residues: 1.4671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 5571 Z= 0.344 Angle : 0.552 5.727 7548 Z= 0.300 Chirality : 0.049 0.180 936 Planarity : 0.003 0.034 960 Dihedral : 4.425 15.971 750 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.67 % Favored : 97.19 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 711 helix: 0.01 (0.63), residues: 60 sheet: 0.40 (0.30), residues: 297 loop : -0.78 (0.33), residues: 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.702 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.1740 time to fit residues: 18.4843 Evaluate side-chains 75 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0583 time to fit residues: 1.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.115786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105205 restraints weight = 7285.856| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.62 r_work: 0.2993 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5571 Z= 0.251 Angle : 0.496 5.452 7548 Z= 0.273 Chirality : 0.048 0.152 936 Planarity : 0.003 0.032 960 Dihedral : 4.241 15.554 750 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.25 % Favored : 97.61 % Rotamer Outliers : 0.16 % 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: -0.29 (0.31), residues: 711 helix: 0.13 (0.64), residues: 60 sheet: 0.43 (0.30), residues: 297 loop : -0.76 (0.33), residues: 354 =============================================================================== Job complete usr+sys time: 1249.37 seconds wall clock time: 23 minutes 19.50 seconds (1399.50 seconds total)