Starting phenix.real_space_refine on Tue Feb 13 10:51:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/02_2024/8a02_15045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/02_2024/8a02_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_15045/02_2024/8a02_15045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/02_2024/8a02_15045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/02_2024/8a02_15045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a02_15045/02_2024/8a02_15045.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5238/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: 3.68, per 1000 atoms: 0.67 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.79 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: 1.55 Time building geometry restraints manager: 2.06 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: 0.330 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: 2.050 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.500 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- 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 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 118 PHE 0.009 0.001 PHE D 231 TYR 0.012 0.001 TYR E 43 ARG 0.002 0.000 ARG D 114 *********************** 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 : 0.678 Fit side-chains REVERT: F 155 ILE cc_start: 0.8606 (mt) cc_final: 0.8355 (mt) REVERT: D 110 ILE cc_start: 0.9032 (mm) cc_final: 0.8752 (mt) REVERT: D 147 ASP cc_start: 0.7550 (t70) cc_final: 0.7279 (t70) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1598 time to fit residues: 23.5340 Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.8248 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 5571 Z= 0.440 Angle : 0.628 5.990 7548 Z= 0.336 Chirality : 0.052 0.169 936 Planarity : 0.004 0.033 960 Dihedral : 4.640 17.732 750 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 2.38 % Allowed : 11.59 % Favored : 86.03 % 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: -0.32 (0.31), residues: 711 helix: 0.29 (0.65), residues: 60 sheet: 0.36 (0.30), residues: 300 loop : -0.76 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.010 0.002 PHE F 63 TYR 0.019 0.002 TYR E 43 ARG 0.002 0.000 ARG E 187 *********************** 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 107 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.693 Fit side-chains REVERT: E 1 MET cc_start: 0.7652 (pmm) cc_final: 0.7206 (ptt) REVERT: D 110 ILE cc_start: 0.9082 (mm) cc_final: 0.8803 (mt) REVERT: D 188 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7984 (t0) outliers start: 15 outliers final: 13 residues processed: 104 average time/residue: 0.1584 time to fit residues: 22.3508 Evaluate side-chains 93 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 188 ASP 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: 2.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5571 Z= 0.206 Angle : 0.475 5.284 7548 Z= 0.261 Chirality : 0.047 0.153 936 Planarity : 0.003 0.030 960 Dihedral : 4.171 14.690 750 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.75 % Allowed : 17.62 % Favored : 80.63 % 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: -0.19 (0.31), residues: 711 helix: 0.54 (0.66), residues: 60 sheet: 0.45 (0.30), residues: 300 loop : -0.72 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.008 0.001 PHE D 231 TYR 0.014 0.001 TYR E 43 ARG 0.001 0.000 ARG D 114 *********************** 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 102 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.637 Fit side-chains REVERT: F 176 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8757 (ttpt) REVERT: E 1 MET cc_start: 0.7610 (pmm) cc_final: 0.7221 (ptt) REVERT: D 110 ILE cc_start: 0.9083 (mm) cc_final: 0.8747 (mt) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.1649 time to fit residues: 21.7989 Evaluate side-chains 94 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN D 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 5571 Z= 0.513 Angle : 0.654 6.118 7548 Z= 0.349 Chirality : 0.052 0.169 936 Planarity : 0.004 0.037 960 Dihedral : 4.804 15.987 750 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 4.29 % Allowed : 17.78 % Favored : 77.94 % 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: -0.62 (0.30), residues: 711 helix: -0.22 (0.63), residues: 60 sheet: 0.28 (0.30), residues: 297 loop : -1.01 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 118 PHE 0.012 0.002 PHE F 63 TYR 0.019 0.002 TYR E 43 ARG 0.002 0.001 ARG F 114 *********************** 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 106 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 0.643 Fit side-chains REVERT: F 107 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: E 1 MET cc_start: 0.7642 (pmm) cc_final: 0.7283 (ptt) REVERT: E 136 SER cc_start: 0.8845 (m) cc_final: 0.8485 (m) REVERT: E 164 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6862 (t70) REVERT: D 110 ILE cc_start: 0.9089 (mm) cc_final: 0.8795 (mt) outliers start: 27 outliers final: 18 residues processed: 97 average time/residue: 0.1586 time to fit residues: 20.5696 Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 164 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5571 Z= 0.356 Angle : 0.562 6.027 7548 Z= 0.305 Chirality : 0.050 0.159 936 Planarity : 0.004 0.034 960 Dihedral : 4.600 16.266 750 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.39 % Favored : 97.33 % Rotamer: Outliers : 4.13 % Allowed : 19.68 % Favored : 76.19 % 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: -0.65 (0.31), residues: 711 helix: -0.22 (0.64), residues: 60 sheet: 0.26 (0.30), residues: 297 loop : -1.04 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.009 0.002 PHE D 231 TYR 0.019 0.002 TYR E 43 ARG 0.002 0.000 ARG E 187 *********************** 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 104 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.692 Fit side-chains REVERT: F 107 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: E 1 MET cc_start: 0.7615 (pmm) cc_final: 0.7316 (ptt) REVERT: E 82 MET cc_start: 0.8146 (tmm) cc_final: 0.7557 (ttp) REVERT: D 110 ILE cc_start: 0.9149 (mm) cc_final: 0.8846 (mt) outliers start: 26 outliers final: 19 residues processed: 95 average time/residue: 0.1613 time to fit residues: 20.5698 Evaluate side-chains 96 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5571 Z= 0.177 Angle : 0.460 5.257 7548 Z= 0.254 Chirality : 0.047 0.149 936 Planarity : 0.003 0.030 960 Dihedral : 4.148 16.166 750 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.65 % Allowed : 21.43 % Favored : 74.92 % 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: -0.37 (0.31), residues: 711 helix: 0.14 (0.65), residues: 60 sheet: 0.40 (0.30), residues: 297 loop : -0.84 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.008 0.001 PHE D 231 TYR 0.013 0.001 TYR E 43 ARG 0.001 0.000 ARG E 46 *********************** 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 105 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.675 Fit side-chains REVERT: F 107 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: E 1 MET cc_start: 0.7587 (pmm) cc_final: 0.7326 (ptt) REVERT: E 59 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8630 (mp) REVERT: D 110 ILE cc_start: 0.9094 (mm) cc_final: 0.8753 (mt) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.1490 time to fit residues: 19.9902 Evaluate side-chains 103 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP 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: 8.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5571 Z= 0.297 Angle : 0.528 5.920 7548 Z= 0.287 Chirality : 0.049 0.156 936 Planarity : 0.003 0.031 960 Dihedral : 4.365 16.300 750 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 4.44 % Allowed : 20.95 % Favored : 74.60 % 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: -0.46 (0.31), residues: 711 helix: -0.04 (0.64), residues: 60 sheet: 0.33 (0.30), residues: 297 loop : -0.87 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.010 0.001 PHE D 231 TYR 0.018 0.002 TYR E 43 ARG 0.001 0.000 ARG E 46 *********************** 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 107 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.600 Fit side-chains REVERT: F 107 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: E 1 MET cc_start: 0.7603 (pmm) cc_final: 0.7317 (ptt) REVERT: E 59 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8590 (mp) REVERT: E 82 MET cc_start: 0.8117 (tmm) cc_final: 0.7501 (ttp) REVERT: E 209 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8192 (tp) REVERT: D 110 ILE cc_start: 0.9101 (mm) cc_final: 0.8785 (mt) outliers start: 28 outliers final: 20 residues processed: 100 average time/residue: 0.1513 time to fit residues: 20.3062 Evaluate side-chains 98 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5571 Z= 0.109 Angle : 0.419 4.846 7548 Z= 0.233 Chirality : 0.046 0.143 936 Planarity : 0.003 0.029 960 Dihedral : 3.774 16.102 750 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.75 % Allowed : 23.65 % Favored : 74.60 % 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: -0.15 (0.32), residues: 711 helix: 0.39 (0.65), residues: 60 sheet: 0.49 (0.30), residues: 297 loop : -0.66 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 118 PHE 0.008 0.001 PHE E 231 TYR 0.011 0.001 TYR E 43 ARG 0.001 0.000 ARG D 46 *********************** 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 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.672 Fit side-chains REVERT: E 1 MET cc_start: 0.7545 (pmm) cc_final: 0.7320 (ptt) REVERT: D 110 ILE cc_start: 0.9040 (mm) cc_final: 0.8678 (mt) REVERT: D 189 ILE cc_start: 0.7866 (mm) cc_final: 0.7637 (mt) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.1673 time to fit residues: 20.4587 Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 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: 0.8212 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5571 Z= 0.216 Angle : 0.478 5.458 7548 Z= 0.262 Chirality : 0.047 0.152 936 Planarity : 0.003 0.029 960 Dihedral : 4.023 15.943 750 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.86 % Allowed : 22.70 % Favored : 74.44 % 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: -0.15 (0.32), residues: 711 helix: 0.29 (0.64), residues: 60 sheet: 0.51 (0.30), residues: 297 loop : -0.66 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.015 0.001 TYR E 43 ARG 0.001 0.000 ARG E 187 *********************** 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 105 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.687 Fit side-chains REVERT: E 1 MET cc_start: 0.7575 (pmm) cc_final: 0.7315 (ptt) REVERT: E 59 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8640 (mp) REVERT: D 110 ILE cc_start: 0.9066 (mm) cc_final: 0.8739 (mt) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.1412 time to fit residues: 19.2137 Evaluate side-chains 102 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 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: 0.5980 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5571 Z= 0.398 Angle : 0.590 5.768 7548 Z= 0.319 Chirality : 0.050 0.176 936 Planarity : 0.003 0.033 960 Dihedral : 4.564 16.402 750 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 3.49 % Allowed : 22.38 % Favored : 74.13 % 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: -0.47 (0.31), residues: 711 helix: -0.21 (0.62), residues: 60 sheet: 0.33 (0.30), residues: 297 loop : -0.84 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.013 0.002 PHE D 231 TYR 0.019 0.002 TYR E 43 ARG 0.003 0.000 ARG E 187 ********************** 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 95 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.671 Fit side-chains REVERT: E 1 MET cc_start: 0.7622 (pmm) cc_final: 0.7336 (ptt) REVERT: E 59 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8591 (mp) REVERT: E 82 MET cc_start: 0.8118 (tmm) cc_final: 0.7502 (ttp) REVERT: D 110 ILE cc_start: 0.9093 (mm) cc_final: 0.8806 (mt) outliers start: 22 outliers final: 19 residues processed: 90 average time/residue: 0.1588 time to fit residues: 19.3212 Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.115322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.105105 restraints weight = 7340.715| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.59 r_work: 0.2997 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5571 Z= 0.188 Angle : 0.471 5.151 7548 Z= 0.260 Chirality : 0.047 0.149 936 Planarity : 0.003 0.031 960 Dihedral : 4.144 15.971 750 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.02 % Allowed : 22.54 % Favored : 74.44 % 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: 0.06 (0.64), residues: 60 sheet: 0.42 (0.30), residues: 297 loop : -0.76 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.013 0.001 TYR E 43 ARG 0.002 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.49 seconds wall clock time: 23 minutes 51.59 seconds (1431.59 seconds total)