Starting phenix.real_space_refine on Thu Dec 7 21:35:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/12_2023/8ey2_28666.pdb" } resolution = 3.5 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= 1.000 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 46 5.16 5 C 3108 2.51 5 N 836 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 197": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Time building chain proxies: 5.26, per 1000 atoms: 1.07 Number of scatterers: 4908 At special positions: 0 Unit cell: (72.483, 86.849, 74.442, 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 46 16.00 O 918 8.00 N 836 7.00 C 3108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.549A pdb=" N MET B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 118 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.949A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.120A pdb=" N LYS B 102 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.904A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 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: 1.28 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1612 1.34 - 1.46: 1160 1.46 - 1.58: 2176 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 5016 Sorted by residual: bond pdb=" CG LEU B 32 " pdb=" CD1 LEU B 32 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB MET A 264 " pdb=" CG MET A 264 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CG LEU B 272 " pdb=" CD1 LEU B 272 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CG LEU C -1 " pdb=" CD2 LEU C -1 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.25: 82 104.25 - 111.68: 2314 111.68 - 119.10: 1694 119.10 - 126.53: 2660 126.53 - 133.96: 60 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA LEU C -1 " pdb=" CB LEU C -1 " pdb=" CG LEU C -1 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA LEU D -1 " pdb=" CB LEU D -1 " pdb=" CG LEU D -1 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" C VAL C -2 " pdb=" N LEU C -1 " pdb=" CA LEU C -1 " ideal model delta sigma weight residual 121.26 124.71 -3.45 1.59e+00 3.96e-01 4.70e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 2616 14.12 - 28.24: 240 28.24 - 42.35: 88 42.35 - 56.47: 12 56.47 - 70.59: 6 Dihedral angle restraints: 2962 sinusoidal: 1142 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 0 " pdb=" C GLN C 0 " pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C -1 " pdb=" C LEU C -1 " pdb=" N GLN C 0 " pdb=" CA GLN C 0 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA THR B 175 " pdb=" C THR B 175 " pdb=" N ASP B 176 " pdb=" CA ASP B 176 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 447 0.031 - 0.062: 218 0.062 - 0.093: 74 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CG LEU D -1 " pdb=" CB LEU D -1 " pdb=" CD1 LEU D -1 " pdb=" CD2 LEU D -1 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA VAL C -2 " pdb=" N VAL C -2 " pdb=" C VAL C -2 " pdb=" CB VAL C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 765 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 51 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 52 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " 0.011 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 3 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.002 2.00e-02 2.50e+03 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 4949 3.25 - 3.80: 8026 3.80 - 4.35: 10191 4.35 - 4.90: 17041 Nonbonded interactions: 40341 Sorted by model distance: nonbonded pdb=" OG1 THR A 292 " pdb=" OD2 ASP A 295 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR A 209 " pdb=" OG SER A 254 " model vdw 2.177 2.440 nonbonded pdb=" O THR A 26 " pdb=" OG SER C 1 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR B 45 " pdb=" OD1 ASP B 48 " model vdw 2.217 2.440 ... (remaining 40336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 116 or resid 118 through 306)) selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.17 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: 0.490 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: 2.640 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.930 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.034 5016 Z= 0.189 Angle : 0.600 9.693 6810 Z= 0.315 Chirality : 0.042 0.154 768 Planarity : 0.005 0.055 884 Dihedral : 13.039 70.588 1798 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.35), residues: 628 helix: 1.88 (0.44), residues: 150 sheet: -1.02 (0.54), residues: 102 loop : -0.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.026 0.001 PHE D 3 TYR 0.024 0.002 TYR A 239 ARG 0.002 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1757 time to fit residues: 38.3808 Evaluate side-chains 130 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5016 Z= 0.224 Angle : 0.691 10.757 6810 Z= 0.345 Chirality : 0.044 0.153 768 Planarity : 0.005 0.045 884 Dihedral : 5.081 20.480 680 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.75 % Allowed : 13.37 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.33), residues: 628 helix: 0.96 (0.39), residues: 170 sheet: -1.08 (0.53), residues: 102 loop : -0.97 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.006 0.001 HIS B 41 PHE 0.015 0.001 PHE D 3 TYR 0.013 0.002 TYR B 209 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.1513 time to fit residues: 26.2633 Evaluate side-chains 126 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0483 time to fit residues: 1.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 0.0370 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5016 Z= 0.359 Angle : 0.721 8.965 6810 Z= 0.370 Chirality : 0.045 0.178 768 Planarity : 0.005 0.043 884 Dihedral : 5.398 23.356 680 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 2.93 % Allowed : 16.30 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.33), residues: 628 helix: 1.03 (0.41), residues: 158 sheet: -1.64 (0.58), residues: 80 loop : -0.94 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.006 0.002 HIS B 41 PHE 0.015 0.002 PHE B 181 TYR 0.022 0.003 TYR B 161 ARG 0.003 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.1332 time to fit residues: 21.7500 Evaluate side-chains 119 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.559 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.0497 time to fit residues: 1.9968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5016 Z= 0.205 Angle : 0.632 10.360 6810 Z= 0.319 Chirality : 0.042 0.127 768 Planarity : 0.004 0.038 884 Dihedral : 5.247 23.448 680 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 1.47 % Allowed : 16.85 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.33), residues: 628 helix: 1.13 (0.40), residues: 170 sheet: -1.50 (0.60), residues: 80 loop : -0.86 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 PHE 0.014 0.001 PHE A 181 TYR 0.028 0.002 TYR B 161 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.537 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.1537 time to fit residues: 23.5141 Evaluate side-chains 109 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0500 time to fit residues: 1.2246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5016 Z= 0.240 Angle : 0.664 10.828 6810 Z= 0.334 Chirality : 0.042 0.142 768 Planarity : 0.004 0.036 884 Dihedral : 5.270 22.974 680 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 1.10 % Allowed : 18.32 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.32), residues: 628 helix: 1.03 (0.39), residues: 172 sheet: -2.44 (0.65), residues: 56 loop : -0.93 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 PHE 0.012 0.001 PHE A 181 TYR 0.031 0.002 TYR B 161 ARG 0.001 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.520 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 115 average time/residue: 0.1364 time to fit residues: 21.1871 Evaluate side-chains 111 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0522 time to fit residues: 1.2108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5016 Z= 0.198 Angle : 0.655 11.476 6810 Z= 0.327 Chirality : 0.042 0.188 768 Planarity : 0.004 0.038 884 Dihedral : 5.227 24.800 680 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.92 % Allowed : 19.78 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 628 helix: 1.03 (0.39), residues: 174 sheet: -2.39 (0.66), residues: 56 loop : -0.94 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 218 HIS 0.006 0.001 HIS A 41 PHE 0.012 0.001 PHE B 181 TYR 0.031 0.002 TYR B 161 ARG 0.002 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.560 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 0.1330 time to fit residues: 19.6869 Evaluate side-chains 106 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0559 time to fit residues: 1.1382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5016 Z= 0.178 Angle : 0.658 14.135 6810 Z= 0.330 Chirality : 0.043 0.238 768 Planarity : 0.004 0.038 884 Dihedral : 5.159 24.613 680 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.92 % Allowed : 21.25 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.32), residues: 628 helix: 1.10 (0.39), residues: 174 sheet: -2.40 (0.63), residues: 60 loop : -1.05 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.006 0.001 HIS B 41 PHE 0.010 0.001 PHE A 181 TYR 0.031 0.002 TYR B 161 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.523 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 112 average time/residue: 0.1397 time to fit residues: 21.2100 Evaluate side-chains 109 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0546 time to fit residues: 1.1597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5016 Z= 0.183 Angle : 0.651 12.965 6810 Z= 0.328 Chirality : 0.043 0.263 768 Planarity : 0.004 0.038 884 Dihedral : 5.158 22.871 680 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.10 % Allowed : 22.53 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.33), residues: 628 helix: 1.03 (0.40), residues: 172 sheet: -2.36 (0.64), residues: 60 loop : -1.02 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 218 HIS 0.007 0.001 HIS B 41 PHE 0.017 0.001 PHE A 223 TYR 0.029 0.002 TYR B 161 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.556 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.1345 time to fit residues: 20.6361 Evaluate side-chains 108 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0490 time to fit residues: 1.0115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5016 Z= 0.200 Angle : 0.656 13.545 6810 Z= 0.330 Chirality : 0.043 0.247 768 Planarity : 0.004 0.038 884 Dihedral : 5.213 25.804 680 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.73 % Allowed : 24.36 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.33), residues: 628 helix: 1.15 (0.40), residues: 172 sheet: -2.42 (0.62), residues: 60 loop : -1.06 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 207 HIS 0.005 0.001 HIS A 163 PHE 0.025 0.001 PHE A 140 TYR 0.027 0.002 TYR B 161 ARG 0.003 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.588 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 0.1316 time to fit residues: 20.6948 Evaluate side-chains 109 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0625 time to fit residues: 0.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 7 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5016 Z= 0.180 Angle : 0.659 13.266 6810 Z= 0.331 Chirality : 0.042 0.169 768 Planarity : 0.004 0.038 884 Dihedral : 5.182 25.723 680 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.37 % Allowed : 25.46 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.33), residues: 628 helix: 1.30 (0.40), residues: 170 sheet: -2.39 (0.62), residues: 60 loop : -1.17 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.009 0.001 HIS B 41 PHE 0.022 0.001 PHE A 140 TYR 0.028 0.002 TYR B 161 ARG 0.004 0.000 ARG C 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.527 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1295 time to fit residues: 19.7269 Evaluate side-chains 105 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0764 time to fit residues: 0.8166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.0040 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122122 restraints weight = 17517.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127892 restraints weight = 6228.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131545 restraints weight = 3227.800| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5016 Z= 0.173 Angle : 0.619 7.788 6810 Z= 0.319 Chirality : 0.042 0.140 768 Planarity : 0.004 0.038 884 Dihedral : 5.027 24.915 680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.18 % Allowed : 25.64 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.33), residues: 628 helix: 1.36 (0.40), residues: 170 sheet: -2.35 (0.62), residues: 60 loop : -1.21 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.004 0.001 HIS A 163 PHE 0.022 0.001 PHE A 140 TYR 0.027 0.002 TYR B 161 ARG 0.004 0.000 ARG C 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.38 seconds wall clock time: 26 minutes 21.38 seconds (1581.38 seconds total)