Starting phenix.real_space_refine on Fri Dec 27 11:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkx_27493/12_2024/8dkx_27493.cif" } resolution = 3.0 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= 0.004 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.44, per 1000 atoms: 0.79 Number of scatterers: 4370 At special positions: 0 Unit cell: (76.36, 63.91, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 788 8.00 N 704 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 539.3 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 35.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.914A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 153 removed outlier: 4.187A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.591A pdb=" N VAL P 206 " --> pdb=" O ASN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 291 Proline residue: P 283 - end of helix removed outlier: 3.751A pdb=" N PHE P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.554A pdb=" N PHE P 311 " --> pdb=" O THR P 307 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET P 316 " --> pdb=" O SER P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.423A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 33 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.928A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.696A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.418A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.805A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.513A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 54 through 56 218 hydrogen bonds defined for protein. 621 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: 1.20 Time building geometry restraints manager: 1.21 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: 1343 1.34 - 1.46: 1039 1.46 - 1.58: 2086 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.445 1.478 -0.033 8.30e-03 1.45e+04 1.60e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.56e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.83e-02 2.99e+03 1.87e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 6042 2.73 - 5.46: 66 5.46 - 8.19: 10 8.19 - 10.92: 3 10.92 - 13.64: 1 Bond angle restraints: 6122 Sorted by residual: angle pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" C THR P 261 " ideal model delta sigma weight residual 113.02 121.82 -8.80 1.20e+00 6.94e-01 5.38e+01 angle pdb=" N TRP P 262 " pdb=" CA TRP P 262 " pdb=" C TRP P 262 " ideal model delta sigma weight residual 113.20 99.56 13.64 2.08e+00 2.31e-01 4.30e+01 angle pdb=" N GLY P 258 " pdb=" CA GLY P 258 " pdb=" C GLY P 258 " ideal model delta sigma weight residual 111.20 119.74 -8.54 1.39e+00 5.18e-01 3.77e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 113.20 109.16 4.04 9.60e-01 1.09e+00 1.77e+01 angle pdb=" CA VAL P 259 " pdb=" C VAL P 259 " pdb=" O VAL P 259 " ideal model delta sigma weight residual 121.17 117.07 4.10 1.06e+00 8.90e-01 1.50e+01 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 2312 17.22 - 34.44: 228 34.44 - 51.66: 37 51.66 - 68.88: 4 68.88 - 86.10: 2 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C ILE P 260 " pdb=" N ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual -122.00 -135.90 13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual 123.40 135.21 -11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" CA LYS P 335 " pdb=" C LYS P 335 " pdb=" N PHE P 336 " pdb=" CA PHE P 336 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 609 0.073 - 0.145: 80 0.145 - 0.218: 2 0.218 - 0.291: 0 0.291 - 0.363: 2 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ILE P 260 " pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CB ILE P 260 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 297 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" CG TRP P 297 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP P 297 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 297 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 297 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 259 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C VAL P 259 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL P 259 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE P 260 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 44 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.019 5.00e-02 4.00e+02 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 70 2.66 - 3.22: 4081 3.22 - 3.78: 6520 3.78 - 4.34: 9227 4.34 - 4.90: 15449 Nonbonded interactions: 35347 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.099 3.040 nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.187 3.120 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.245 3.040 ... (remaining 35342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.050 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.005 0.043 4490 Z= 0.290 Angle : 0.748 13.644 6122 Z= 0.436 Chirality : 0.049 0.363 693 Planarity : 0.004 0.033 764 Dihedral : 13.282 86.102 1557 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.62 % Allowed : 6.43 % Favored : 92.95 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % 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: -3.42 (0.31), residues: 547 helix: -1.19 (0.31), residues: 204 sheet: -2.45 (0.37), residues: 161 loop : -3.10 (0.36), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 PHE 0.020 0.001 PHE P 269 TYR 0.011 0.001 TYR B 49 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.495 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 82 ASP cc_start: 0.7840 (m-30) cc_final: 0.7598 (m-30) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.9337 time to fit residues: 58.0734 Evaluate side-chains 51 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain P residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 111 GLN B 6 GLN B 38 GLN P 96 GLN P 149 ASN P 204 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4490 Z= 0.177 Angle : 0.593 9.880 6122 Z= 0.302 Chirality : 0.043 0.136 693 Planarity : 0.004 0.047 764 Dihedral : 5.686 56.583 599 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.49 % Allowed : 13.49 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.85 (0.34), residues: 547 helix: 0.33 (0.35), residues: 206 sheet: -1.65 (0.41), residues: 147 loop : -2.49 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 PHE 0.019 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.003 0.000 ARG P 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.496 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 71 GLU cc_start: 0.7429 (tt0) cc_final: 0.7159 (tm-30) REVERT: P 269 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.5715 (m-10) outliers start: 12 outliers final: 4 residues processed: 60 average time/residue: 0.9727 time to fit residues: 61.4691 Evaluate side-chains 53 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS P 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4490 Z= 0.406 Angle : 0.694 11.247 6122 Z= 0.352 Chirality : 0.048 0.171 693 Planarity : 0.004 0.029 764 Dihedral : 5.945 48.534 599 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.11 % Allowed : 15.56 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.62 (0.34), residues: 547 helix: 0.50 (0.35), residues: 206 sheet: -1.47 (0.40), residues: 154 loop : -2.41 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 297 HIS 0.003 0.001 HIS P 102 PHE 0.030 0.002 PHE A 69 TYR 0.022 0.002 TYR P 134 ARG 0.006 0.001 ARG P 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.493 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 13 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8051 (mmmt) REVERT: A 106 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8016 (mt) REVERT: B 79 GLN cc_start: 0.8259 (mt0) cc_final: 0.8046 (mm-40) REVERT: P 269 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6156 (m-10) outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.8870 time to fit residues: 58.0037 Evaluate side-chains 53 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7987 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 0.025 4490 Z= 0.186 Angle : 0.586 10.577 6122 Z= 0.294 Chirality : 0.043 0.142 693 Planarity : 0.003 0.029 764 Dihedral : 5.485 43.928 599 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.53 % Allowed : 16.80 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.09 (0.35), residues: 547 helix: 1.05 (0.36), residues: 206 sheet: -1.22 (0.41), residues: 154 loop : -2.24 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.017 0.001 PHE A 69 TYR 0.014 0.001 TYR P 134 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.479 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 3 MET cc_start: 0.7244 (mmm) cc_final: 0.6843 (mpp) REVERT: P 71 GLU cc_start: 0.7402 (tt0) cc_final: 0.7148 (tm-30) REVERT: P 269 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: P 282 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: P 318 LEU cc_start: 0.7450 (pp) cc_final: 0.7108 (tp) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 0.9279 time to fit residues: 62.4944 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 21 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4490 Z= 0.187 Angle : 0.573 9.905 6122 Z= 0.286 Chirality : 0.043 0.138 693 Planarity : 0.003 0.028 764 Dihedral : 5.216 35.507 599 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.94 % Allowed : 16.60 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.81 (0.35), residues: 547 helix: 1.26 (0.36), residues: 206 sheet: -1.02 (0.43), residues: 140 loop : -2.07 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.012 0.001 PHE A 69 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.498 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7973 (mt) REVERT: B 9 SER cc_start: 0.7966 (m) cc_final: 0.7581 (m) REVERT: B 79 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7800 (mm-40) REVERT: P 71 GLU cc_start: 0.7321 (tt0) cc_final: 0.7083 (tm-30) REVERT: P 269 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.5830 (m-10) REVERT: P 282 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: P 318 LEU cc_start: 0.7441 (pp) cc_final: 0.7145 (tp) outliers start: 19 outliers final: 10 residues processed: 64 average time/residue: 0.9072 time to fit residues: 61.2556 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4490 Z= 0.295 Angle : 0.629 10.735 6122 Z= 0.317 Chirality : 0.045 0.157 693 Planarity : 0.003 0.025 764 Dihedral : 5.353 29.337 599 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.53 % Allowed : 17.84 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.95 (0.35), residues: 547 helix: 1.15 (0.36), residues: 206 sheet: -1.11 (0.41), residues: 155 loop : -2.17 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 297 HIS 0.002 0.001 HIS P 102 PHE 0.014 0.001 PHE A 69 TYR 0.020 0.002 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.517 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7958 (mt) REVERT: P 71 GLU cc_start: 0.7326 (tt0) cc_final: 0.7102 (tm-30) REVERT: P 269 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.5982 (m-10) REVERT: P 282 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7415 (m-10) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.8929 time to fit residues: 59.3058 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4490 Z= 0.226 Angle : 0.607 10.032 6122 Z= 0.300 Chirality : 0.044 0.145 693 Planarity : 0.003 0.028 764 Dihedral : 5.095 23.234 597 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.94 % Allowed : 17.63 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.36), residues: 547 helix: 1.24 (0.36), residues: 207 sheet: -1.05 (0.40), residues: 160 loop : -2.05 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 PHE 0.012 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.473 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 3 MET cc_start: 0.7291 (mmm) cc_final: 0.6759 (mpp) REVERT: A 106 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7958 (mt) REVERT: P 71 GLU cc_start: 0.7342 (tt0) cc_final: 0.7137 (tm-30) REVERT: P 269 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5849 (m-10) REVERT: P 282 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7398 (m-10) outliers start: 19 outliers final: 12 residues processed: 64 average time/residue: 0.8651 time to fit residues: 58.2922 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4490 Z= 0.204 Angle : 0.595 11.021 6122 Z= 0.296 Chirality : 0.043 0.142 693 Planarity : 0.003 0.030 764 Dihedral : 5.014 22.660 597 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.11 % Allowed : 18.46 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.36), residues: 547 helix: 1.31 (0.36), residues: 207 sheet: -1.03 (0.40), residues: 160 loop : -2.02 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 PHE 0.009 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.508 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 3 MET cc_start: 0.7203 (mmm) cc_final: 0.6876 (mpp) REVERT: A 106 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7929 (mt) REVERT: B 78 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6633 (mp) REVERT: P 71 GLU cc_start: 0.7351 (tt0) cc_final: 0.7147 (tm-30) REVERT: P 269 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5856 (m-10) REVERT: P 282 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: P 318 LEU cc_start: 0.7488 (pp) cc_final: 0.7179 (tp) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.8740 time to fit residues: 58.1405 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4490 Z= 0.220 Angle : 0.609 10.998 6122 Z= 0.301 Chirality : 0.044 0.143 693 Planarity : 0.004 0.062 764 Dihedral : 5.015 22.742 597 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.94 % Allowed : 18.26 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.68 (0.36), residues: 547 helix: 1.32 (0.36), residues: 207 sheet: -0.95 (0.40), residues: 160 loop : -2.01 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 PHE 0.027 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.013 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.497 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 106 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (mt) REVERT: B 78 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6658 (mp) REVERT: P 71 GLU cc_start: 0.7369 (tt0) cc_final: 0.7165 (tm-30) REVERT: P 269 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: P 282 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: P 318 LEU cc_start: 0.7507 (pp) cc_final: 0.7162 (tp) outliers start: 19 outliers final: 13 residues processed: 61 average time/residue: 0.8586 time to fit residues: 55.4236 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4490 Z= 0.273 Angle : 0.634 11.272 6122 Z= 0.313 Chirality : 0.045 0.153 693 Planarity : 0.004 0.057 764 Dihedral : 5.125 23.363 597 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.15 % Allowed : 18.05 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.36), residues: 547 helix: 1.25 (0.36), residues: 207 sheet: -1.01 (0.40), residues: 160 loop : -2.04 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 297 HIS 0.002 0.001 HIS P 102 PHE 0.029 0.001 PHE A 69 TYR 0.018 0.001 TYR P 134 ARG 0.013 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.568 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 3 MET cc_start: 0.7181 (mmm) cc_final: 0.6790 (mpp) REVERT: A 106 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7949 (mt) REVERT: P 71 GLU cc_start: 0.7390 (tt0) cc_final: 0.7184 (tm-30) REVERT: P 269 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: P 318 LEU cc_start: 0.7522 (pp) cc_final: 0.7106 (tp) outliers start: 20 outliers final: 12 residues processed: 65 average time/residue: 0.9540 time to fit residues: 65.4335 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN P 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127146 restraints weight = 4927.032| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.00 r_work: 0.3358 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4490 Z= 0.165 Angle : 0.595 10.722 6122 Z= 0.291 Chirality : 0.043 0.141 693 Planarity : 0.004 0.064 764 Dihedral : 4.888 22.897 597 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.90 % Allowed : 20.33 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.57 (0.36), residues: 547 helix: 1.45 (0.36), residues: 207 sheet: -0.94 (0.40), residues: 160 loop : -1.95 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 PHE 0.020 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.015 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.22 seconds wall clock time: 31 minutes 58.83 seconds (1918.83 seconds total)