Starting phenix.real_space_refine on Fri Dec 27 14:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a02_15045/12_2024/8a02_15045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a02_15045/12_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/cci-nas-00/data/ceres_data/8a02_15045/12_2024/8a02_15045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a02_15045/12_2024/8a02_15045.map" model { file = "/net/cci-nas-00/data/ceres_data/8a02_15045/12_2024/8a02_15045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a02_15045/12_2024/8a02_15045.cif" } 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. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.06, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 717.3 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: 0.67 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: 1.42 Time building geometry restraints manager: 1.39 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: 0.00 - 1.15: 7320 1.15 - 2.30: 188 2.30 - 3.44: 34 3.44 - 4.59: 4 4.59 - 5.74: 2 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 3.120 nonbonded pdb=" OD1 ASN F 80 " pdb=" NH2 ARG F 114 " model vdw 2.395 3.120 nonbonded pdb=" N GLY D 22 " pdb=" O ILE D 120 " model vdw 2.406 3.120 nonbonded pdb=" O GLU D 140 " pdb=" NE2 GLN D 225 " model vdw 2.409 3.120 nonbonded pdb=" OG SER F 76 " pdb=" N ASP F 77 " model vdw 2.443 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.370 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.632 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: 0.1575 time to fit residues: 23.4137 Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5571 Z= 0.315 Angle : 0.552 5.810 7548 Z= 0.297 Chirality : 0.049 0.164 936 Planarity : 0.003 0.030 960 Dihedral : 4.295 14.863 750 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.75 % Allowed : 10.16 % Favored : 88.10 % 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: -0.05 (0.31), residues: 711 helix: 0.64 (0.66), residues: 60 sheet: 0.54 (0.30), residues: 300 loop : -0.62 (0.33), residues: 351 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 0.017 0.002 TYR E 43 ARG 0.003 0.000 ARG F 114 *********************** 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 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.694 Fit side-chains REVERT: F 100 GLU cc_start: 0.7612 (pt0) cc_final: 0.7230 (pt0) REVERT: F 160 ASP cc_start: 0.7441 (t0) cc_final: 0.7197 (t0) REVERT: E 1 MET cc_start: 0.7618 (pmm) cc_final: 0.7158 (ptt) REVERT: D 110 ILE cc_start: 0.9086 (mm) cc_final: 0.8768 (mt) REVERT: D 188 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7902 (t0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.1618 time to fit residues: 22.7327 Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 158 VAL 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: 9.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.1032 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= 0.218 Angle : 0.487 5.364 7548 Z= 0.266 Chirality : 0.048 0.156 936 Planarity : 0.003 0.030 960 Dihedral : 4.130 14.378 750 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.06 % Allowed : 13.65 % Favored : 84.29 % 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: -0.09 (0.31), residues: 711 helix: 0.63 (0.66), residues: 60 sheet: 0.53 (0.30), residues: 300 loop : -0.66 (0.33), residues: 351 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 0.014 0.001 TYR E 43 ARG 0.001 0.000 ARG F 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 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.656 Fit side-chains REVERT: E 1 MET cc_start: 0.7593 (pmm) cc_final: 0.7204 (ptt) REVERT: D 110 ILE cc_start: 0.9077 (mm) cc_final: 0.8728 (mt) REVERT: D 188 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7993 (t0) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.1447 time to fit residues: 19.6584 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 165 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5571 Z= 0.357 Angle : 0.566 5.973 7548 Z= 0.305 Chirality : 0.050 0.161 936 Planarity : 0.003 0.032 960 Dihedral : 4.498 14.989 750 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 15.71 % Favored : 80.95 % 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: -0.29 (0.31), residues: 711 helix: 0.28 (0.65), residues: 60 sheet: 0.45 (0.30), residues: 297 loop : -0.81 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.010 0.002 PHE D 231 TYR 0.018 0.002 TYR E 43 ARG 0.003 0.000 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 105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.659 Fit side-chains REVERT: F 107 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: E 1 MET cc_start: 0.7613 (pmm) cc_final: 0.7278 (ptt) REVERT: D 110 ILE cc_start: 0.9150 (mm) cc_final: 0.8826 (mt) outliers start: 21 outliers final: 16 residues processed: 98 average time/residue: 0.1639 time to fit residues: 21.6458 Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 143 ASN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 SER 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 136 SER 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 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: 7.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8245 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5571 Z= 0.342 Angle : 0.557 5.901 7548 Z= 0.301 Chirality : 0.049 0.160 936 Planarity : 0.004 0.033 960 Dihedral : 4.528 15.399 750 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 3.33 % Allowed : 17.46 % Favored : 79.21 % 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: -0.44 (0.31), residues: 711 helix: 0.09 (0.64), residues: 60 sheet: 0.36 (0.30), residues: 297 loop : -0.90 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.018 0.002 TYR E 43 ARG 0.003 0.000 ARG F 114 *********************** 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 105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.689 Fit side-chains REVERT: F 107 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: E 1 MET cc_start: 0.7617 (pmm) cc_final: 0.7301 (ptt) REVERT: E 82 MET cc_start: 0.8126 (tmm) cc_final: 0.7519 (ttp) REVERT: D 110 ILE cc_start: 0.9151 (mm) cc_final: 0.8830 (mt) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.1692 time to fit residues: 22.1919 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 98 ASP 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 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 105 THR Chi-restraints excluded: chain D residue 126 THR 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: 4.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5571 Z= 0.279 Angle : 0.520 5.700 7548 Z= 0.284 Chirality : 0.048 0.156 936 Planarity : 0.003 0.033 960 Dihedral : 4.379 14.608 750 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.47 % Rotamer: Outliers : 3.65 % Allowed : 17.94 % Favored : 78.41 % 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: -0.40 (0.31), residues: 711 helix: 0.10 (0.64), residues: 60 sheet: 0.38 (0.30), residues: 297 loop : -0.86 (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 0.016 0.001 TYR E 43 ARG 0.002 0.000 ARG F 114 *********************** 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 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.652 Fit side-chains REVERT: F 107 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: E 1 MET cc_start: 0.7598 (pmm) cc_final: 0.7315 (ptt) REVERT: D 110 ILE cc_start: 0.9131 (mm) cc_final: 0.8804 (mt) outliers start: 23 outliers final: 16 residues processed: 99 average time/residue: 0.1577 time to fit residues: 20.8410 Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 170 SER 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 136 SER Chi-restraints excluded: chain E residue 165 LEU 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 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1515 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 : 0.539 5.858 7548 Z= 0.294 Chirality : 0.049 0.158 936 Planarity : 0.003 0.034 960 Dihedral : 4.442 14.737 750 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 4.29 % Allowed : 17.94 % Favored : 77.78 % 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: -0.45 (0.31), residues: 711 helix: 0.00 (0.63), residues: 60 sheet: 0.36 (0.30), residues: 297 loop : -0.89 (0.32), 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 0.017 0.002 TYR E 43 ARG 0.002 0.000 ARG F 114 *********************** 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 111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.683 Fit side-chains REVERT: F 107 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: E 1 MET cc_start: 0.7602 (pmm) cc_final: 0.7327 (ptt) REVERT: E 59 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 110 ILE cc_start: 0.9132 (mm) cc_final: 0.8813 (mt) REVERT: D 189 ILE cc_start: 0.7789 (mm) cc_final: 0.7559 (mt) outliers start: 27 outliers final: 19 residues processed: 104 average time/residue: 0.1577 time to fit residues: 22.1343 Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 98 ASP 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 170 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR 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 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: 6.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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: 0.8258 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5571 Z= 0.364 Angle : 0.570 5.885 7548 Z= 0.309 Chirality : 0.049 0.161 936 Planarity : 0.004 0.035 960 Dihedral : 4.570 17.011 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 4.13 % Allowed : 18.57 % Favored : 77.30 % 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: -0.58 (0.31), residues: 711 helix: -0.17 (0.63), residues: 60 sheet: 0.27 (0.30), residues: 297 loop : -0.96 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.009 0.001 PHE F 63 TYR 0.017 0.002 TYR E 43 ARG 0.003 0.000 ARG F 114 *********************** 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 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.634 Fit side-chains REVERT: F 107 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: E 1 MET cc_start: 0.7610 (pmm) cc_final: 0.7321 (ptt) REVERT: E 59 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8574 (mp) REVERT: E 82 MET cc_start: 0.8166 (tmm) cc_final: 0.7579 (ttp) REVERT: D 110 ILE cc_start: 0.9129 (mm) cc_final: 0.8822 (mt) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.1481 time to fit residues: 20.1910 Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 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 74 THR Chi-restraints excluded: chain F residue 98 ASP 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 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 10 THR Chi-restraints excluded: chain E residue 59 LEU 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 D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.8225 moved from start: 0.1512 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= 0.217 Angle : 0.489 5.326 7548 Z= 0.269 Chirality : 0.048 0.152 936 Planarity : 0.003 0.032 960 Dihedral : 4.260 16.443 750 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.11 % Favored : 97.75 % Rotamer: Outliers : 3.97 % Allowed : 19.05 % Favored : 76.98 % 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: -0.41 (0.31), residues: 711 helix: 0.07 (0.64), residues: 60 sheet: 0.36 (0.30), residues: 297 loop : -0.85 (0.33), 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 F 114 *********************** 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 to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.760 Fit side-chains REVERT: F 107 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: E 1 MET cc_start: 0.7576 (pmm) cc_final: 0.7344 (ptt) REVERT: E 59 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (mp) REVERT: E 82 MET cc_start: 0.8059 (tmm) cc_final: 0.7454 (ttp) REVERT: D 1 MET cc_start: 0.7188 (pmm) cc_final: 0.5336 (tpt) REVERT: D 110 ILE cc_start: 0.9108 (mm) cc_final: 0.8780 (mt) REVERT: D 189 ILE cc_start: 0.7781 (mm) cc_final: 0.7568 (mt) outliers start: 25 outliers final: 19 residues processed: 98 average time/residue: 0.1448 time to fit residues: 19.6860 Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 98 ASP 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 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR 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 105 THR Chi-restraints excluded: chain D residue 126 THR 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: 0.0370 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 42 optimal weight: 0.0020 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.0270 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5571 Z= 0.130 Angle : 0.436 4.845 7548 Z= 0.242 Chirality : 0.046 0.148 936 Planarity : 0.003 0.031 960 Dihedral : 3.872 15.992 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 20.95 % Favored : 76.98 % 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 (0.32), residues: 711 helix: 0.37 (0.65), residues: 60 sheet: 0.49 (0.30), residues: 297 loop : -0.71 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 118 PHE 0.008 0.001 PHE D 231 TYR 0.011 0.001 TYR E 43 ARG 0.002 0.000 ARG F 114 ********************** 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 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.506 Fit side-chains REVERT: E 1 MET cc_start: 0.7537 (pmm) cc_final: 0.7327 (ptt) REVERT: D 1 MET cc_start: 0.7002 (pmm) cc_final: 0.5291 (tpt) REVERT: D 110 ILE cc_start: 0.9058 (mm) cc_final: 0.8725 (mt) REVERT: D 189 ILE cc_start: 0.7785 (mm) cc_final: 0.7560 (mt) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1533 time to fit residues: 20.9284 Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 143 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 165 LEU 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: 5.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.114428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103040 restraints weight = 7209.535| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.78 r_work: 0.2963 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5571 Z= 0.387 Angle : 0.586 5.696 7548 Z= 0.316 Chirality : 0.050 0.164 936 Planarity : 0.004 0.035 960 Dihedral : 4.508 16.276 750 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 2.70 % Allowed : 20.79 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.31), residues: 711 helix: -0.08 (0.62), residues: 60 sheet: 0.32 (0.30), residues: 297 loop : -0.83 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.009 0.002 PHE F 63 TYR 0.017 0.002 TYR E 43 ARG 0.005 0.001 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.22 seconds wall clock time: 24 minutes 2.64 seconds (1442.64 seconds total)