Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 18:57:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/10_2023/8g92_29860_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.050 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 17 5.16 5 C 2117 2.51 5 N 529 2.21 5 O 548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 534": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3211 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3211 Unusual residues: {'YUX': 1} Classifications: {'peptide': 415, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 402, None: 1} Not linked: pdbres="GLN A 539 " pdbres="YUX A 601 " Chain breaks: 2 Time building chain proxies: 2.19, per 1000 atoms: 0.68 Number of scatterers: 3211 At special positions: 0 Unit cell: (69.72, 64.74, 81.34, 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 17 16.00 O 548 8.00 N 529 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 464.2 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 101 through 121 removed outlier: 3.854A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.717A pdb=" N VAL A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.712A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 removed outlier: 4.153A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 221 removed outlier: 3.600A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 224 through 256 Proline residue: A 239 - end of helix removed outlier: 4.239A pdb=" N TYR A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.947A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 314 through 346 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 388 removed outlier: 4.673A pdb=" N PHE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 418 removed outlier: 3.909A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.723A pdb=" N SER A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.791A pdb=" N ARG A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA A 457 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 494 through 538 removed outlier: 4.111A pdb=" N LEU A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.696A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 726 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: 0.88 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 967 1.34 - 1.46: 545 1.46 - 1.57: 1748 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3286 Sorted by residual: bond pdb=" C ASP A 118 " pdb=" O ASP A 118 " ideal model delta sigma weight residual 1.237 1.251 -0.015 1.16e-02 7.43e+03 1.58e+00 bond pdb=" CA LEU A 161 " pdb=" C LEU A 161 " ideal model delta sigma weight residual 1.522 1.503 0.018 1.72e-02 3.38e+03 1.14e+00 bond pdb=" C ALA A 140 " pdb=" O ALA A 140 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.17e-02 7.31e+03 8.17e-01 bond pdb=" CB VAL A 203 " pdb=" CG2 VAL A 203 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.82e-01 bond pdb=" CA VAL A 125 " pdb=" C VAL A 125 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.42e-01 ... (remaining 3281 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.92: 53 105.92 - 112.94: 1809 112.94 - 119.97: 1157 119.97 - 126.99: 1402 126.99 - 134.01: 37 Bond angle restraints: 4458 Sorted by residual: angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 121.39 -7.79 1.90e+00 2.77e-01 1.68e+01 angle pdb=" C THR A 121 " pdb=" N VAL A 122 " pdb=" CA VAL A 122 " ideal model delta sigma weight residual 121.19 116.43 4.76 1.59e+00 3.96e-01 8.96e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.31 116.15 4.16 1.52e+00 4.33e-01 7.48e+00 angle pdb=" C ALA A 395 " pdb=" N ASP A 396 " pdb=" CA ASP A 396 " ideal model delta sigma weight residual 120.97 124.39 -3.42 1.48e+00 4.57e-01 5.34e+00 angle pdb=" C ARG A 119 " pdb=" N TYR A 120 " pdb=" CA TYR A 120 " ideal model delta sigma weight residual 122.26 118.71 3.55 1.59e+00 3.96e-01 4.98e+00 ... (remaining 4453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1636 14.28 - 28.55: 190 28.55 - 42.83: 51 42.83 - 57.10: 11 57.10 - 71.38: 3 Dihedral angle restraints: 1891 sinusoidal: 708 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG A 264 " pdb=" C ARG A 264 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A 227 " pdb=" CD ARG A 227 " pdb=" NE ARG A 227 " pdb=" CZ ARG A 227 " ideal model delta sinusoidal sigma weight residual -90.00 -134.97 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 340 0.036 - 0.071: 145 0.071 - 0.107: 29 0.107 - 0.143: 7 0.143 - 0.178: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE A 452 " pdb=" N ILE A 452 " pdb=" C ILE A 452 " pdb=" CB ILE A 452 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 519 not shown) Planarity restraints: 542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.018 2.00e-02 2.50e+03 1.23e-02 3.80e+00 pdb=" CG TRP A 178 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 267 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 178 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TRP A 178 " -0.023 2.00e-02 2.50e+03 pdb=" O TRP A 178 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 179 " 0.008 2.00e-02 2.50e+03 ... (remaining 539 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 608 2.75 - 3.29: 3348 3.29 - 3.83: 5553 3.83 - 4.36: 6378 4.36 - 4.90: 10835 Nonbonded interactions: 26722 Sorted by model distance: nonbonded pdb=" O GLY A 219 " pdb=" NH1 ARG A 227 " model vdw 2.219 2.520 nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.235 2.440 nonbonded pdb=" NH2 ARG A 487 " pdb=" OD2 ASP A 492 " model vdw 2.302 2.520 nonbonded pdb=" OG SER A 250 " pdb=" OG SER A 363 " model vdw 2.315 2.440 nonbonded pdb=" O THR A 223 " pdb=" N ARG A 227 " model vdw 2.324 2.520 ... (remaining 26717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.580 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 0.033 3286 Z= 0.324 Angle : 0.656 7.787 4458 Z= 0.377 Chirality : 0.040 0.178 522 Planarity : 0.004 0.038 542 Dihedral : 13.687 71.381 1133 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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: -1.13 (0.38), residues: 409 helix: -0.45 (0.25), residues: 356 sheet: None (None), residues: 0 loop : -1.68 (0.82), residues: 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1634 time to fit residues: 17.4480 Evaluate side-chains 63 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 190 GLN A 254 GLN A 539 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3286 Z= 0.249 Angle : 0.593 7.339 4458 Z= 0.317 Chirality : 0.039 0.166 522 Planarity : 0.005 0.036 542 Dihedral : 5.897 44.975 457 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.87 % Allowed : 16.07 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.41), residues: 409 helix: 0.63 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.68 (1.00), residues: 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1170 time to fit residues: 11.6888 Evaluate side-chains 75 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0372 time to fit residues: 1.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3286 Z= 0.216 Angle : 0.581 9.030 4458 Z= 0.299 Chirality : 0.039 0.159 522 Planarity : 0.005 0.034 542 Dihedral : 5.788 45.174 457 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 18.45 % Favored : 79.46 % 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: 1.33 (0.43), residues: 409 helix: 1.19 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.37 (1.02), residues: 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.395 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.1102 time to fit residues: 10.2577 Evaluate side-chains 68 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0350 time to fit residues: 0.7078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3286 Z= 0.194 Angle : 0.585 7.309 4458 Z= 0.293 Chirality : 0.039 0.151 522 Planarity : 0.004 0.034 542 Dihedral : 5.647 44.698 457 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.08 % Allowed : 18.15 % Favored : 79.76 % 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: 1.72 (0.43), residues: 409 helix: 1.42 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.01 (1.07), residues: 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.347 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 69 average time/residue: 0.1083 time to fit residues: 9.9316 Evaluate side-chains 66 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0354 time to fit residues: 0.9310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- 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: 0.7882 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3286 Z= 0.268 Angle : 0.610 7.249 4458 Z= 0.309 Chirality : 0.041 0.180 522 Planarity : 0.004 0.035 542 Dihedral : 5.832 45.209 457 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.79 % Allowed : 21.13 % Favored : 77.08 % 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: 1.66 (0.43), residues: 409 helix: 1.39 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.07 (1.05), residues: 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.343 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1159 time to fit residues: 9.6524 Evaluate side-chains 63 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0348 time to fit residues: 0.7940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3286 Z= 0.222 Angle : 0.590 8.560 4458 Z= 0.297 Chirality : 0.039 0.159 522 Planarity : 0.004 0.034 542 Dihedral : 5.766 45.435 457 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.89 % Allowed : 23.21 % Favored : 75.89 % 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: 1.79 (0.43), residues: 409 helix: 1.48 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.04 (1.03), residues: 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.361 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.1122 time to fit residues: 9.4256 Evaluate side-chains 62 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0382 time to fit residues: 0.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7865 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3286 Z= 0.254 Angle : 0.641 9.037 4458 Z= 0.322 Chirality : 0.041 0.165 522 Planarity : 0.004 0.035 542 Dihedral : 5.820 45.772 457 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.19 % Allowed : 24.40 % Favored : 74.40 % 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: 1.72 (0.43), residues: 409 helix: 1.42 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.09 (1.06), residues: 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.365 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.1134 time to fit residues: 9.8453 Evaluate side-chains 64 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0373 time to fit residues: 0.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3286 Z= 0.227 Angle : 0.627 9.203 4458 Z= 0.312 Chirality : 0.040 0.158 522 Planarity : 0.004 0.033 542 Dihedral : 5.777 45.519 457 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.19 % Allowed : 24.40 % Favored : 74.40 % 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: 1.87 (0.43), residues: 409 helix: 1.51 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.90 (1.07), residues: 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.347 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.1087 time to fit residues: 9.3685 Evaluate side-chains 67 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0349 time to fit residues: 0.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3286 Z= 0.219 Angle : 0.630 9.000 4458 Z= 0.312 Chirality : 0.041 0.183 522 Planarity : 0.004 0.033 542 Dihedral : 5.724 45.564 457 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.60 % Allowed : 25.30 % Favored : 74.11 % 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: 1.89 (0.43), residues: 409 helix: 1.54 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.93 (1.07), residues: 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.337 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.1069 time to fit residues: 9.5147 Evaluate side-chains 65 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0342 time to fit residues: 0.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3286 Z= 0.248 Angle : 0.655 9.051 4458 Z= 0.322 Chirality : 0.041 0.163 522 Planarity : 0.004 0.034 542 Dihedral : 5.829 45.779 457 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.43), residues: 409 helix: 1.52 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.95 (1.00), residues: 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1142 time to fit residues: 9.9360 Evaluate side-chains 62 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.167112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127421 restraints weight = 4387.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131537 restraints weight = 2671.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134240 restraints weight = 1992.515| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3286 Z= 0.220 Angle : 0.642 9.149 4458 Z= 0.315 Chirality : 0.040 0.155 522 Planarity : 0.004 0.034 542 Dihedral : 5.734 45.794 457 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.30 % Allowed : 25.30 % Favored : 74.40 % 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: 1.87 (0.43), residues: 409 helix: 1.56 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.96 (0.97), residues: 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1035.54 seconds wall clock time: 19 minutes 33.08 seconds (1173.08 seconds total)