Starting phenix.real_space_refine on Thu Dec 7 16:24:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkg_14041/12_2023/7qkg_14041.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 744 2.51 5 N 213 2.21 5 O 228 1.98 5 H 1278 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 314": "OD1" <-> "OD2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "C ASP 314": "OD1" <-> "OD2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2469 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Time building chain proxies: 1.44, per 1000 atoms: 0.58 Number of scatterers: 2469 At special positions: 0 Unit cell: (74.984, 67.568, 35.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 228 8.00 N 213 7.00 C 744 6.00 H 1278 1.00 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: 1.70 Conformation dependent library (CDL) restraints added in 393.8 milliseconds 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 278 removed outlier: 6.492A pdb=" N ILE B 277 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.833A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 291 removed outlier: 9.111A pdb=" N ASN B 286 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER A 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 288 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N CYS A 291 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 290 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN C 288 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.504A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.527A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.516A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.401A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.70 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1272 1.12 - 1.29: 201 1.29 - 1.47: 335 1.47 - 1.64: 664 1.64 - 1.81: 6 Bond restraints: 2478 Sorted by residual: bond pdb=" CE1 TYR A 310 " pdb=" HE1 TYR A 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN B 327 " pdb=" H ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL A 287 " pdb=" H VAL A 287 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 289 " pdb=" H SER A 289 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN C 286 " pdb="HD21 ASN C 286 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 2473 not shown) Histogram of bond angle deviations from ideal: 96.46 - 103.17: 12 103.17 - 109.88: 2202 109.88 - 116.59: 1149 116.59 - 123.30: 1017 123.30 - 130.01: 153 Bond angle restraints: 4533 Sorted by residual: angle pdb=" CA ILE B 328 " pdb=" CB ILE B 328 " pdb=" CG1 ILE B 328 " ideal model delta sigma weight residual 110.40 118.04 -7.64 1.70e+00 3.46e-01 2.02e+01 angle pdb=" N PRO C 312 " pdb=" CA PRO C 312 " pdb=" CB PRO C 312 " ideal model delta sigma weight residual 103.31 107.26 -3.95 8.90e-01 1.26e+00 1.97e+01 angle pdb=" OE1 GLN C 276 " pdb=" CD GLN C 276 " pdb=" NE2 GLN C 276 " ideal model delta sigma weight residual 122.60 118.23 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N PRO A 312 " pdb=" CA PRO A 312 " pdb=" CB PRO A 312 " ideal model delta sigma weight residual 103.31 107.19 -3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" CA VAL B 287 " pdb=" C VAL B 287 " pdb=" N GLN B 288 " ideal model delta sigma weight residual 116.40 121.27 -4.87 1.12e+00 7.97e-01 1.89e+01 ... (remaining 4528 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.90: 977 13.90 - 27.79: 72 27.79 - 41.67: 21 41.67 - 55.56: 7 55.56 - 69.45: 27 Dihedral angle restraints: 1104 sinusoidal: 633 harmonic: 471 Sorted by residual: dihedral pdb=" CA ILE A 297 " pdb=" C ILE A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL A 313 " pdb=" C VAL A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA VAL C 313 " pdb=" C VAL C 313 " pdb=" N ASP C 314 " pdb=" CA ASP C 314 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 1101 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.069: 119 0.069 - 0.138: 47 0.138 - 0.207: 19 0.207 - 0.275: 6 0.275 - 0.344: 4 Chirality restraints: 195 Sorted by residual: chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS A 311 " pdb=" N LYS A 311 " pdb=" C LYS A 311 " pdb=" CB LYS A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 192 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 307 " 0.082 2.00e-02 2.50e+03 8.02e-02 9.65e+01 pdb=" CD GLN B 307 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN B 307 " -0.079 2.00e-02 2.50e+03 pdb=" NE2 GLN B 307 " 0.025 2.00e-02 2.50e+03 pdb="HE21 GLN B 307 " -0.116 2.00e-02 2.50e+03 pdb="HE22 GLN B 307 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 297 " -0.031 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" N LYS B 298 " 0.098 2.00e-02 2.50e+03 pdb=" CA LYS B 298 " -0.028 2.00e-02 2.50e+03 pdb=" H LYS B 298 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 313 " -0.030 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" N ASP A 314 " 0.097 2.00e-02 2.50e+03 pdb=" CA ASP A 314 " -0.028 2.00e-02 2.50e+03 pdb=" H ASP A 314 " -0.040 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 209 2.17 - 2.78: 4235 2.78 - 3.39: 6470 3.39 - 3.99: 8308 3.99 - 4.60: 11399 Nonbonded interactions: 30621 Sorted by model distance: nonbonded pdb=" OD1 ASP A 283 " pdb=" HG SER A 285 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASP B 283 " pdb=" HG SER B 285 " model vdw 1.576 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP C 283 " pdb=" HG SER C 285 " model vdw 1.636 1.850 ... (remaining 30616 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' selection = chain 'B' selection = chain 'C' } 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: 1.470 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: 0.040 Extract box with map and model: 6.520 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.000 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.010 0.036 1200 Z= 0.707 Angle : 2.027 8.738 1608 Z= 1.320 Chirality : 0.101 0.344 195 Planarity : 0.008 0.025 201 Dihedral : 10.758 42.499 462 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.98 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 299 TYR 0.041 0.010 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.215 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.4272 time to fit residues: 12.0071 Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS A 299 HIS C 299 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 1200 Z= 0.223 Angle : 0.691 5.364 1608 Z= 0.352 Chirality : 0.052 0.132 195 Planarity : 0.003 0.017 201 Dihedral : 6.210 22.074 162 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.69 % Allowed : 10.42 % Favored : 88.89 % 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: -2.23 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.014 0.004 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.203 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.4319 time to fit residues: 9.9061 Evaluate side-chains 12 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1200 Z= 0.193 Angle : 0.592 4.616 1608 Z= 0.306 Chirality : 0.053 0.136 195 Planarity : 0.004 0.032 201 Dihedral : 5.589 19.239 162 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % 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: -2.11 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.011 0.003 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.211 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.4414 time to fit residues: 7.7561 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 1200 Z= 0.192 Angle : 0.557 4.310 1608 Z= 0.282 Chirality : 0.052 0.131 195 Planarity : 0.004 0.031 201 Dihedral : 5.364 17.997 162 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.39 % Allowed : 14.58 % Favored : 84.03 % 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: -2.00 (0.59), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.008 0.002 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.206 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.3249 time to fit residues: 5.1754 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0381 time to fit residues: 0.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1200 Z= 0.144 Angle : 0.548 4.258 1608 Z= 0.273 Chirality : 0.052 0.129 195 Planarity : 0.004 0.032 201 Dihedral : 4.959 16.324 162 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -1.95 (0.60), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.006 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3041 time to fit residues: 5.5808 Evaluate side-chains 13 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1200 Z= 0.174 Angle : 0.562 4.629 1608 Z= 0.279 Chirality : 0.052 0.133 195 Planarity : 0.004 0.030 201 Dihedral : 4.977 15.570 162 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -1.91 (0.60), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.007 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3144 time to fit residues: 5.3844 Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1200 Z= 0.131 Angle : 0.509 4.563 1608 Z= 0.255 Chirality : 0.052 0.129 195 Planarity : 0.004 0.031 201 Dihedral : 4.750 16.631 162 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % 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: -1.71 (0.61), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.007 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.226 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.3162 time to fit residues: 5.4110 Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0398 time to fit residues: 0.3222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.0050 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1200 Z= 0.122 Angle : 0.496 4.285 1608 Z= 0.246 Chirality : 0.052 0.130 195 Planarity : 0.004 0.029 201 Dihedral : 4.561 16.213 162 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % 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: -1.55 (0.61), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 299 TYR 0.006 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3119 time to fit residues: 5.3485 Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1200 Z= 0.174 Angle : 0.511 4.306 1608 Z= 0.258 Chirality : 0.052 0.136 195 Planarity : 0.004 0.030 201 Dihedral : 4.740 16.118 162 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -1.57 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.005 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3131 time to fit residues: 5.3504 Evaluate side-chains 14 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1200 Z= 0.134 Angle : 0.495 4.121 1608 Z= 0.247 Chirality : 0.052 0.131 195 Planarity : 0.004 0.030 201 Dihedral : 4.624 16.186 162 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % 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: -1.53 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 299 TYR 0.006 0.001 TYR B 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3100 time to fit residues: 5.2771 Evaluate side-chains 14 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.160037 restraints weight = 4628.033| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.09 r_work: 0.4578 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4494 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1200 Z= 0.115 Angle : 0.481 4.020 1608 Z= 0.240 Chirality : 0.052 0.132 195 Planarity : 0.004 0.030 201 Dihedral : 4.491 16.673 162 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % 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: -1.43 (0.63), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.006 0.001 TYR B 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.62 seconds wall clock time: 35 minutes 54.02 seconds (2154.02 seconds total)