Starting phenix.real_space_refine on Thu Dec 7 19:34:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk8_32562/12_2023/7wk8_32562.pdb" } resolution = 3.61 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= 0.000 sd= 0.011 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 16 5.16 5 C 2512 2.51 5 N 671 2.21 5 O 783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3982 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 150 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Time building chain proxies: 2.62, per 1000 atoms: 0.66 Number of scatterers: 3982 At special positions: 0 Unit cell: (96.184, 95.091, 61.208, 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 16 16.00 O 783 8.00 N 671 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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: 1.37 Conformation dependent library (CDL) restraints added in 832.5 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 3.3% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 127 through 132 removed outlier: 4.250A pdb=" N SER D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 132' Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.977A pdb=" N ARG D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.571A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.570A pdb=" N VAL C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 92 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET C 34 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N MET C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.570A pdb=" N VAL C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 92 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG C 98 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.775A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 182 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.584A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 21 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS D 23 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 76 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.580A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 51 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.580A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS D 94 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA D 101 " --> pdb=" O HIS D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.741A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER D 180 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 166 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.897A pdb=" N TYR D 196 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 213 " --> pdb=" O TYR D 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.538A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 315 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: 1.04 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1262 1.35 - 1.46: 998 1.46 - 1.58: 1799 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4081 Sorted by residual: bond pdb=" N LEU C 184 " pdb=" CA LEU C 184 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.18e+00 bond pdb=" N THR C 183 " pdb=" CA THR C 183 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.26e-02 6.30e+03 7.73e+00 bond pdb=" C GLU D 109 " pdb=" N ILE D 110 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.32e-02 5.74e+03 6.18e+00 bond pdb=" N SER C 119 " pdb=" CA SER C 119 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" N SER C 185 " pdb=" CA SER C 185 " ideal model delta sigma weight residual 1.464 1.487 -0.024 1.25e-02 6.40e+03 3.57e+00 ... (remaining 4076 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.46: 202 107.46 - 114.09: 2268 114.09 - 120.71: 1491 120.71 - 127.33: 1538 127.33 - 133.95: 58 Bond angle restraints: 5557 Sorted by residual: angle pdb=" C SER C 179 " pdb=" N ASP C 180 " pdb=" CA ASP C 180 " ideal model delta sigma weight residual 122.07 127.27 -5.20 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C ALA C 137 " pdb=" N GLN C 138 " pdb=" CA GLN C 138 " ideal model delta sigma weight residual 122.07 127.19 -5.12 1.43e+00 4.89e-01 1.28e+01 angle pdb=" C ILE D 154 " pdb=" N ASP D 155 " pdb=" CA ASP D 155 " ideal model delta sigma weight residual 122.19 127.23 -5.04 1.41e+00 5.03e-01 1.28e+01 angle pdb=" C ASP D 174 " pdb=" N SER D 175 " pdb=" CA SER D 175 " ideal model delta sigma weight residual 122.19 127.16 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C ASN C 162 " pdb=" N SER C 163 " pdb=" CA SER C 163 " ideal model delta sigma weight residual 122.34 127.21 -4.87 1.39e+00 5.18e-01 1.23e+01 ... (remaining 5552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.81: 2296 11.81 - 23.62: 110 23.62 - 35.43: 33 35.43 - 47.24: 17 47.24 - 59.05: 1 Dihedral angle restraints: 2457 sinusoidal: 955 harmonic: 1502 Sorted by residual: dihedral pdb=" CA TRP C 195 " pdb=" C TRP C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR C 101 " pdb=" C TYR C 101 " pdb=" N ASP C 102 " pdb=" CA ASP C 102 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS A 535 " pdb=" C LYS A 535 " pdb=" N ASN A 536 " pdb=" CA ASN A 536 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 532 0.066 - 0.132: 79 0.132 - 0.199: 10 0.199 - 0.265: 2 0.265 - 0.331: 2 Chirality restraints: 625 Sorted by residual: chirality pdb=" CB ILE D 121 " pdb=" CA ILE D 121 " pdb=" CG1 ILE D 121 " pdb=" CG2 ILE D 121 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL C 188 " pdb=" CA VAL C 188 " pdb=" CG1 VAL C 188 " pdb=" CG2 VAL C 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL C 204 " pdb=" CA VAL C 204 " pdb=" CG1 VAL C 204 " pdb=" CG2 VAL C 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 622 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 118 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C VAL C 118 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL C 118 " 0.027 2.00e-02 2.50e+03 pdb=" N SER C 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 195 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO C 196 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 204 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C VAL C 204 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 204 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 205 " 0.014 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 749 2.79 - 3.32: 3126 3.32 - 3.84: 6244 3.84 - 4.37: 6603 4.37 - 4.90: 11958 Nonbonded interactions: 28680 Sorted by model distance: nonbonded pdb=" OG SER D 22 " pdb=" OD1 ASP D 74 " model vdw 2.262 2.440 nonbonded pdb=" OD1 ASN C 61 " pdb=" N GLN C 62 " model vdw 2.374 2.520 nonbonded pdb=" O PRO C 7 " pdb=" OG1 THR C 114 " model vdw 2.393 2.440 nonbonded pdb=" OG SER D 205 " pdb=" O SER D 207 " model vdw 2.396 2.440 nonbonded pdb=" O ALA C 105 " pdb=" OG SER D 95 " model vdw 2.403 2.440 ... (remaining 28675 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 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 group one per residue 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: 1.920 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: 9.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.004 0.054 4081 Z= 0.264 Angle : 0.743 10.268 5557 Z= 0.419 Chirality : 0.054 0.331 625 Planarity : 0.006 0.070 712 Dihedral : 8.507 59.046 1472 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.31), residues: 508 helix: -4.97 (0.38), residues: 8 sheet: -0.12 (0.30), residues: 220 loop : -1.41 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 39 HIS 0.002 0.001 HIS D 193 PHE 0.021 0.002 PHE D 143 TYR 0.014 0.001 TYR C 103 ARG 0.004 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.463 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1685 time to fit residues: 19.7562 Evaluate side-chains 78 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.0050 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.0000 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 178 GLN D 6 GLN B 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4081 Z= 0.195 Angle : 0.527 5.197 5557 Z= 0.271 Chirality : 0.043 0.163 625 Planarity : 0.004 0.040 712 Dihedral : 4.109 26.253 551 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.17 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 6.21 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.52 (0.34), residues: 508 helix: -3.89 (0.94), residues: 8 sheet: 0.43 (0.32), residues: 224 loop : -0.89 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 39 HIS 0.004 0.001 HIS D 202 PHE 0.010 0.002 PHE C 153 TYR 0.013 0.001 TYR D 53 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.464 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.1552 time to fit residues: 17.2962 Evaluate side-chains 77 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0414 time to fit residues: 0.8022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4081 Z= 0.230 Angle : 0.546 6.329 5557 Z= 0.276 Chirality : 0.043 0.156 625 Planarity : 0.004 0.036 712 Dihedral : 4.237 26.038 551 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.36 % Favored : 97.44 % Rotamer: Outliers : 1.77 % Allowed : 7.54 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.07 (0.35), residues: 508 helix: -2.54 (1.66), residues: 8 sheet: 0.82 (0.34), residues: 214 loop : -0.65 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 39 HIS 0.005 0.002 HIS D 193 PHE 0.009 0.002 PHE C 153 TYR 0.011 0.001 TYR C 80 ARG 0.004 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.492 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1703 time to fit residues: 16.9559 Evaluate side-chains 78 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0455 time to fit residues: 1.1299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 4081 Z= 0.338 Angle : 0.587 5.859 5557 Z= 0.302 Chirality : 0.044 0.140 625 Planarity : 0.004 0.031 712 Dihedral : 4.480 25.905 551 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.33 % Allowed : 10.42 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.36), residues: 508 helix: -2.23 (1.78), residues: 8 sheet: 0.99 (0.35), residues: 207 loop : -0.61 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 39 HIS 0.006 0.002 HIS D 80 PHE 0.013 0.002 PHE C 153 TYR 0.013 0.002 TYR C 80 ARG 0.003 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.489 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1535 time to fit residues: 15.5403 Evaluate side-chains 79 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0368 time to fit residues: 0.8724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 40 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN A 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 4081 Z= 0.325 Angle : 0.587 5.814 5557 Z= 0.304 Chirality : 0.044 0.163 625 Planarity : 0.004 0.030 712 Dihedral : 4.564 25.257 551 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 0.89 % Allowed : 12.86 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.07 (0.35), residues: 508 helix: -1.78 (2.03), residues: 8 sheet: 0.90 (0.35), residues: 209 loop : -0.72 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 39 HIS 0.006 0.002 HIS D 80 PHE 0.012 0.002 PHE C 153 TYR 0.012 0.002 TYR C 80 ARG 0.003 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.416 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.1590 time to fit residues: 14.6163 Evaluate side-chains 70 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0397 time to fit residues: 0.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4081 Z= 0.205 Angle : 0.525 5.883 5557 Z= 0.269 Chirality : 0.043 0.139 625 Planarity : 0.004 0.031 712 Dihedral : 4.277 24.135 551 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.95 % Favored : 96.85 % Rotamer: Outliers : 0.44 % Allowed : 14.19 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.36), residues: 508 helix: -1.55 (2.06), residues: 8 sheet: 0.92 (0.34), residues: 219 loop : -0.60 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 39 HIS 0.003 0.001 HIS D 202 PHE 0.007 0.001 PHE C 153 TYR 0.007 0.001 TYR D 53 ARG 0.001 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.478 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.1570 time to fit residues: 13.7893 Evaluate side-chains 67 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0378 time to fit residues: 0.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4081 Z= 0.309 Angle : 0.580 6.188 5557 Z= 0.299 Chirality : 0.044 0.144 625 Planarity : 0.004 0.034 712 Dihedral : 4.500 25.443 551 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 1.33 % Allowed : 13.97 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.04 (0.36), residues: 508 helix: -1.37 (2.26), residues: 8 sheet: 0.97 (0.35), residues: 213 loop : -0.68 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 39 HIS 0.005 0.001 HIS D 202 PHE 0.011 0.002 PHE C 153 TYR 0.011 0.002 TYR C 80 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.435 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1542 time to fit residues: 14.4835 Evaluate side-chains 75 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0388 time to fit residues: 0.8768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.0170 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4081 Z= 0.247 Angle : 0.538 5.158 5557 Z= 0.278 Chirality : 0.043 0.141 625 Planarity : 0.004 0.029 712 Dihedral : 4.365 24.982 551 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 0.67 % Allowed : 14.19 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.10 (0.36), residues: 508 helix: -1.54 (2.12), residues: 8 sheet: 1.06 (0.35), residues: 214 loop : -0.69 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 39 HIS 0.004 0.001 HIS D 202 PHE 0.009 0.001 PHE C 153 TYR 0.008 0.001 TYR C 80 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.475 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.1738 time to fit residues: 15.2284 Evaluate side-chains 71 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0423 time to fit residues: 0.8967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 46 optimal weight: 0.0470 chunk 22 optimal weight: 0.0170 chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4081 Z= 0.229 Angle : 0.528 5.197 5557 Z= 0.271 Chirality : 0.042 0.141 625 Planarity : 0.004 0.029 712 Dihedral : 4.290 24.782 551 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 0.67 % Allowed : 13.97 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.17 (0.37), residues: 508 helix: -1.33 (2.18), residues: 8 sheet: 1.15 (0.35), residues: 215 loop : -0.69 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 39 HIS 0.004 0.001 HIS D 202 PHE 0.009 0.001 PHE C 153 TYR 0.007 0.001 TYR C 182 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.448 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.1821 time to fit residues: 16.5050 Evaluate side-chains 73 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0442 time to fit residues: 0.7453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4081 Z= 0.314 Angle : 0.584 5.488 5557 Z= 0.303 Chirality : 0.044 0.144 625 Planarity : 0.004 0.030 712 Dihedral : 4.511 25.327 551 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.36), residues: 508 helix: -2.48 (1.65), residues: 8 sheet: 1.13 (0.35), residues: 215 loop : -0.78 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 106 HIS 0.005 0.001 HIS D 202 PHE 0.011 0.002 PHE C 153 TYR 0.011 0.002 TYR C 80 ARG 0.002 0.000 ARG D 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.509 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1700 time to fit residues: 17.4651 Evaluate side-chains 78 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 0.0070 chunk 31 optimal weight: 0.0170 chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 overall best weight: 0.0834 ------------------------------------------------------------------------------- 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 = 0.3013 r_free = 0.3013 target = 0.091889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.080201 restraints weight = 7250.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.082407 restraints weight = 4024.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.083865 restraints weight = 2647.461| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4081 Z= 0.130 Angle : 0.530 7.586 5557 Z= 0.262 Chirality : 0.043 0.153 625 Planarity : 0.003 0.031 712 Dihedral : 4.142 26.060 551 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.56 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.37), residues: 508 helix: -2.65 (1.73), residues: 8 sheet: 1.18 (0.34), residues: 221 loop : -0.56 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 39 HIS 0.002 0.001 HIS C 206 PHE 0.005 0.001 PHE C 29 TYR 0.008 0.001 TYR D 53 ARG 0.002 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1349.82 seconds wall clock time: 24 minutes 59.93 seconds (1499.93 seconds total)