Starting phenix.real_space_refine (version: dev) on Fri Feb 17 17:05:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/02_2023/7fci_31526.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 147": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5613 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2280 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1640 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1693 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Time building chain proxies: 3.82, per 1000 atoms: 0.68 Number of scatterers: 5613 At special positions: 0 Unit cell: (57.201, 66.32, 135.127, 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 47 16.00 O 1045 8.00 N 899 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 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: 2.35 Conformation dependent library (CDL) restraints added in 869.1 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 41.4% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 removed outlier: 3.900A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.544A pdb=" N LYS A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.569A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 216 removed outlier: 3.824A pdb=" N MET A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.689A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.566A pdb=" N ASP L 81 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.775A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.057A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 195 through 200 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.778A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.620A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.852A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.703A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER H 188 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'H' and resid 178 through 180 331 hydrogen bonds defined for protein. 915 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: 1.63 Time building geometry restraints manager: 2.38 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: 1549 1.34 - 1.45: 1038 1.45 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5749 Sorted by residual: bond pdb=" CB PRO A 220 " pdb=" CG PRO A 220 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG PRO L 94 " pdb=" CD PRO L 94 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.09e+00 bond pdb=" CA VAL H 159 " pdb=" CB VAL H 159 " ideal model delta sigma weight residual 1.551 1.540 0.011 1.08e-02 8.57e+03 9.47e-01 bond pdb=" CA VAL H 106 " pdb=" CB VAL H 106 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.47e-02 4.63e+03 9.15e-01 ... (remaining 5744 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 190 106.29 - 113.23: 3167 113.23 - 120.17: 1892 120.17 - 127.11: 2501 127.11 - 134.05: 67 Bond angle restraints: 7817 Sorted by residual: angle pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA LEU A 165 " pdb=" CB LEU A 165 " pdb=" CG LEU A 165 " ideal model delta sigma weight residual 116.30 126.33 -10.03 3.50e+00 8.16e-02 8.21e+00 angle pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.70e+00 3.46e-01 6.68e+00 angle pdb=" CA TYR L 31 " pdb=" CB TYR L 31 " pdb=" CG TYR L 31 " ideal model delta sigma weight residual 113.90 118.30 -4.40 1.80e+00 3.09e-01 5.97e+00 angle pdb=" CA GLY H 115 " pdb=" C GLY H 115 " pdb=" O GLY H 115 " ideal model delta sigma weight residual 122.22 120.63 1.59 6.50e-01 2.37e+00 5.95e+00 ... (remaining 7812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2913 16.35 - 32.69: 367 32.69 - 49.04: 124 49.04 - 65.38: 28 65.38 - 81.73: 4 Dihedral angle restraints: 3436 sinusoidal: 1310 harmonic: 2126 Sorted by residual: dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 160.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CA ASN L 30 " pdb=" C ASN L 30 " pdb=" N TYR L 31 " pdb=" CA TYR L 31 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLY A 132 " pdb=" C GLY A 132 " pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 533 0.027 - 0.054: 241 0.054 - 0.080: 70 0.080 - 0.107: 44 0.107 - 0.134: 20 Chirality restraints: 908 Sorted by residual: chirality pdb=" CA VAL H 206 " pdb=" N VAL H 206 " pdb=" C VAL H 206 " pdb=" CB VAL H 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL H 161 " pdb=" N VAL H 161 " pdb=" C VAL H 161 " pdb=" CB VAL H 161 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 905 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 208 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO H 209 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 209 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 209 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.046 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 220 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO A 181 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.035 5.00e-02 4.00e+02 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1142 2.78 - 3.31: 4982 3.31 - 3.84: 9209 3.84 - 4.37: 10533 4.37 - 4.90: 18948 Nonbonded interactions: 44814 Sorted by model distance: nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLN A 68 " pdb=" OG SER A 126 " model vdw 2.260 2.440 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.266 2.440 nonbonded pdb=" OG SER L 120 " pdb=" O PRO H 132 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG L 107 " pdb=" O ASP L 169 " model vdw 2.271 2.520 ... (remaining 44809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 3622 2.51 5 N 899 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 4.190 Check model and map are aligned: 0.090 Process input model: 19.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 0.066 5749 Z= 0.180 Angle : 0.596 10.026 7817 Z= 0.317 Chirality : 0.040 0.134 908 Planarity : 0.006 0.096 965 Dihedral : 16.431 81.730 2062 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.59 (0.32), residues: 728 helix: 1.93 (0.34), residues: 258 sheet: 0.27 (0.38), residues: 198 loop : -1.02 (0.37), residues: 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 0.738 Fit side-chains outliers start: 29 outliers final: 25 residues processed: 98 average time/residue: 0.1454 time to fit residues: 20.3840 Evaluate side-chains 97 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0595 time to fit residues: 3.8578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.197 Angle : 0.539 8.141 7817 Z= 0.275 Chirality : 0.041 0.147 908 Planarity : 0.006 0.067 965 Dihedral : 4.742 69.485 781 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.76 (0.33), residues: 728 helix: 1.99 (0.33), residues: 266 sheet: 0.19 (0.36), residues: 221 loop : -0.83 (0.41), residues: 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.615 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 0.1476 time to fit residues: 19.8028 Evaluate side-chains 83 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0597 time to fit residues: 2.2471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5749 Z= 0.277 Angle : 0.565 6.901 7817 Z= 0.290 Chirality : 0.042 0.149 908 Planarity : 0.005 0.059 965 Dihedral : 4.885 69.652 781 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.72 (0.32), residues: 728 helix: 1.89 (0.32), residues: 266 sheet: 0.24 (0.36), residues: 221 loop : -0.85 (0.41), residues: 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.724 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 0.1365 time to fit residues: 16.1544 Evaluate side-chains 77 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0506 time to fit residues: 1.0915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.181 Angle : 0.529 6.904 7817 Z= 0.269 Chirality : 0.040 0.148 908 Planarity : 0.005 0.052 965 Dihedral : 4.770 69.778 781 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.83 (0.32), residues: 728 helix: 2.02 (0.32), residues: 266 sheet: 0.29 (0.36), residues: 221 loop : -0.83 (0.41), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.587 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 84 average time/residue: 0.1340 time to fit residues: 15.5667 Evaluate side-chains 74 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0699 time to fit residues: 0.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 5749 Z= 0.445 Angle : 0.649 8.060 7817 Z= 0.332 Chirality : 0.045 0.159 908 Planarity : 0.006 0.051 965 Dihedral : 5.173 69.528 781 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.48 (0.32), residues: 728 helix: 1.66 (0.32), residues: 266 sheet: 0.19 (0.36), residues: 219 loop : -1.00 (0.40), residues: 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.643 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 99 average time/residue: 0.1491 time to fit residues: 20.6272 Evaluate side-chains 83 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0596 time to fit residues: 1.8051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5749 Z= 0.300 Angle : 0.599 8.674 7817 Z= 0.303 Chirality : 0.043 0.156 908 Planarity : 0.005 0.053 965 Dihedral : 5.046 69.712 781 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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 (0.32), residues: 728 helix: 1.67 (0.32), residues: 266 sheet: 0.15 (0.36), residues: 219 loop : -1.01 (0.40), residues: 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.658 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.1587 time to fit residues: 18.2500 Evaluate side-chains 78 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0549 time to fit residues: 1.3371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.203 Angle : 0.576 9.728 7817 Z= 0.286 Chirality : 0.041 0.148 908 Planarity : 0.005 0.052 965 Dihedral : 4.887 69.944 781 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.61 (0.32), residues: 728 helix: 1.84 (0.32), residues: 266 sheet: 0.20 (0.36), residues: 223 loop : -0.99 (0.41), residues: 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.629 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.1511 time to fit residues: 15.7271 Evaluate side-chains 72 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0577 time to fit residues: 1.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.188 Angle : 0.565 10.053 7817 Z= 0.281 Chirality : 0.041 0.148 908 Planarity : 0.005 0.051 965 Dihedral : 4.821 70.095 781 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.73 (0.33), residues: 728 helix: 1.96 (0.32), residues: 266 sheet: 0.26 (0.36), residues: 223 loop : -0.93 (0.41), residues: 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.739 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1463 time to fit residues: 15.2100 Evaluate side-chains 73 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0697 time to fit residues: 1.0776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 10.0000 chunk 38 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.201 Angle : 0.586 10.813 7817 Z= 0.290 Chirality : 0.041 0.145 908 Planarity : 0.005 0.051 965 Dihedral : 4.862 70.160 781 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.71 (0.33), residues: 728 helix: 1.93 (0.32), residues: 266 sheet: 0.25 (0.36), residues: 223 loop : -0.94 (0.41), residues: 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1585 time to fit residues: 16.8027 Evaluate side-chains 74 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7649 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5749 Z= 0.261 Angle : 0.609 11.183 7817 Z= 0.303 Chirality : 0.042 0.149 908 Planarity : 0.005 0.050 965 Dihedral : 4.976 70.119 781 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.59 (0.32), residues: 728 helix: 1.82 (0.32), residues: 266 sheet: 0.18 (0.36), residues: 223 loop : -0.99 (0.41), residues: 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.764 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.1467 time to fit residues: 15.5159 Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0593 time to fit residues: 1.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.169794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132217 restraints weight = 6004.671| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.48 r_work: 0.2881 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5749 Z= 0.186 Angle : 0.585 10.993 7817 Z= 0.289 Chirality : 0.041 0.145 908 Planarity : 0.005 0.051 965 Dihedral : 4.891 70.211 781 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.69 (0.33), residues: 728 helix: 1.92 (0.32), residues: 265 sheet: 0.24 (0.36), residues: 223 loop : -0.95 (0.41), residues: 240 =============================================================================== Job complete usr+sys time: 1382.13 seconds wall clock time: 26 minutes 5.41 seconds (1565.41 seconds total)