Starting phenix.real_space_refine on Sun Mar 10 20:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afx_15411/03_2024/8afx_15411.pdb" } resolution = 4.8 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2498 atoms to isotropic. 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 1603 2.51 5 N 406 2.21 5 O 472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2498 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2498 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 4 Time building chain proxies: 1.88, per 1000 atoms: 0.75 Number of scatterers: 2498 At special positions: 0 Unit cell: (68.7898, 65.4342, 69.6287, 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 472 8.00 N 406 7.00 C 1603 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: 0.85 Conformation dependent library (CDL) restraints added in 473.8 milliseconds 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 4.119A pdb=" N PHE A 10 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 23 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 12 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 40 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN A 32 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 38 " --> pdb=" O ASN A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.755A pdb=" N VAL A 62 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 50 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 60 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 75 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU A 88 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 77 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 84 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 108 removed outlier: 7.134A pdb=" N ILE A 113 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 126 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 115 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.556A pdb=" N TYR A 150 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLY A 225 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A 242 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 227 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 240 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 229 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 236 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.211A pdb=" N ALA A 263 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET A 251 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 261 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 253 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 259 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 271 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 264 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 269 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 282 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP A 274 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS A 280 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 298 removed outlier: 6.991A pdb=" N THR A 308 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 296 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 306 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE A 298 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 304 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 309 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 316 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 413 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.571A pdb=" N ARG A 468 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 462 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 437 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.571A pdb=" N ARG A 468 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 478 " --> pdb=" O LEU A 492 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 165 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: 0.68 Time building geometry restraints manager: 0.94 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: 784 1.34 - 1.46: 559 1.46 - 1.58: 1170 1.58 - 1.70: 2 1.70 - 1.81: 30 Bond restraints: 2545 Sorted by residual: bond pdb=" CB PRO A 483 " pdb=" CG PRO A 483 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.03e+01 bond pdb=" N PRO A 483 " pdb=" CA PRO A 483 " ideal model delta sigma weight residual 1.470 1.446 0.025 1.01e-02 9.80e+03 5.90e+00 bond pdb=" CB PRO A 141 " pdb=" CG PRO A 141 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.86e+00 bond pdb=" N PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 1.473 1.499 -0.026 1.40e-02 5.10e+03 3.58e+00 bond pdb=" CG PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 1.503 1.446 0.057 3.40e-02 8.65e+02 2.81e+00 ... (remaining 2540 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.03: 27 103.03 - 110.82: 886 110.82 - 118.61: 1125 118.61 - 126.40: 1381 126.40 - 134.20: 23 Bond angle restraints: 3442 Sorted by residual: angle pdb=" CA PRO A 483 " pdb=" N PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 112.00 95.24 16.76 1.40e+00 5.10e-01 1.43e+02 angle pdb=" N PRO A 483 " pdb=" CD PRO A 483 " pdb=" CG PRO A 483 " ideal model delta sigma weight residual 103.20 95.59 7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C PRO A 483 " pdb=" CA PRO A 483 " pdb=" CB PRO A 483 " ideal model delta sigma weight residual 110.00 114.53 -4.53 1.12e+00 7.97e-01 1.64e+01 angle pdb=" CA PRO A 141 " pdb=" N PRO A 141 " pdb=" CD PRO A 141 " ideal model delta sigma weight residual 112.00 106.66 5.34 1.40e+00 5.10e-01 1.46e+01 angle pdb=" CA LEU A 417 " pdb=" CB LEU A 417 " pdb=" CG LEU A 417 " ideal model delta sigma weight residual 116.30 128.37 -12.07 3.50e+00 8.16e-02 1.19e+01 ... (remaining 3437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1315 16.68 - 33.36: 178 33.36 - 50.04: 38 50.04 - 66.72: 6 66.72 - 83.40: 3 Dihedral angle restraints: 1540 sinusoidal: 610 harmonic: 930 Sorted by residual: dihedral pdb=" CA MET A 462 " pdb=" C MET A 462 " pdb=" N LYS A 463 " pdb=" CA LYS A 463 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 98 " pdb=" C VAL A 98 " pdb=" N LYS A 99 " pdb=" CA LYS A 99 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 284 0.047 - 0.094: 85 0.094 - 0.141: 36 0.141 - 0.188: 0 0.188 - 0.235: 1 Chirality restraints: 406 Sorted by residual: chirality pdb=" CA PRO A 483 " pdb=" N PRO A 483 " pdb=" C PRO A 483 " pdb=" CB PRO A 483 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 403 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 483 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 417 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 418 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 140 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " -0.022 5.00e-02 4.00e+02 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 123 2.71 - 3.26: 2430 3.26 - 3.80: 3814 3.80 - 4.35: 4506 4.35 - 4.90: 7520 Nonbonded interactions: 18393 Sorted by model distance: nonbonded pdb=" OG SER A 471 " pdb=" OD1 ASP A 473 " model vdw 2.159 2.440 nonbonded pdb=" OG SER A 57 " pdb=" OD1 ASN A 79 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASN A 101 " pdb=" N SER A 103 " model vdw 2.234 2.520 nonbonded pdb=" OG SER A 44 " pdb=" OH TYR A 47 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASN A 14 " pdb=" N GLY A 17 " model vdw 2.238 2.520 ... (remaining 18388 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 3.520 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.200 Find NCS groups from input model: 0.080 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 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 0.160 2545 Z= 0.292 Angle : 0.901 16.763 3442 Z= 0.482 Chirality : 0.051 0.235 406 Planarity : 0.007 0.114 430 Dihedral : 16.079 83.399 940 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.05 % Allowed : 28.22 % Favored : 70.73 % 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: -0.47 (0.46), residues: 311 helix: None (None), residues: 0 sheet: 1.07 (0.45), residues: 121 loop : -1.34 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 411 PHE 0.019 0.002 PHE A 317 TYR 0.018 0.002 TYR A 116 ARG 0.003 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.350 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.1213 time to fit residues: 10.7504 Evaluate side-chains 64 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.6634 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2545 Z= 0.216 Angle : 0.628 6.954 3442 Z= 0.319 Chirality : 0.049 0.155 406 Planarity : 0.004 0.045 430 Dihedral : 5.129 19.551 342 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -0.37 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 1.15 (0.44), residues: 122 loop : -1.28 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 315 PHE 0.012 0.002 PHE A 39 TYR 0.008 0.001 TYR A 116 ARG 0.004 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9165 (mm) cc_final: 0.8675 (mm) REVERT: A 319 LEU cc_start: 0.7504 (mt) cc_final: 0.7226 (mt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1203 time to fit residues: 12.2858 Evaluate side-chains 64 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.6621 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2545 Z= 0.197 Angle : 0.647 7.100 3442 Z= 0.317 Chirality : 0.050 0.178 406 Planarity : 0.004 0.033 430 Dihedral : 4.969 18.684 342 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -0.63 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.76 (0.44), residues: 124 loop : -1.32 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.021 0.002 PHE A 13 TYR 0.009 0.001 TYR A 116 ARG 0.003 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7497 (tmtt) cc_final: 0.7262 (tmtt) REVERT: A 136 LEU cc_start: 0.9053 (mm) cc_final: 0.8493 (mm) REVERT: A 296 ILE cc_start: 0.8988 (mm) cc_final: 0.8468 (pt) REVERT: A 319 LEU cc_start: 0.7566 (mt) cc_final: 0.7287 (mt) REVERT: A 464 MET cc_start: 0.7454 (mmp) cc_final: 0.7167 (mmp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1226 time to fit residues: 12.1811 Evaluate side-chains 64 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 30 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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: 0.6576 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2545 Z= 0.168 Angle : 0.629 7.482 3442 Z= 0.306 Chirality : 0.051 0.152 406 Planarity : 0.004 0.047 430 Dihedral : 4.735 19.453 342 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.46 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 1.03 (0.46), residues: 112 loop : -1.18 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 315 PHE 0.029 0.002 PHE A 317 TYR 0.008 0.001 TYR A 116 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.8015 (m) cc_final: 0.7745 (m) REVERT: A 34 GLU cc_start: 0.8424 (tp30) cc_final: 0.7813 (tm-30) REVERT: A 136 LEU cc_start: 0.9025 (mm) cc_final: 0.8472 (mm) REVERT: A 223 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7848 (tppt) REVERT: A 286 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7554 (tmm-80) REVERT: A 296 ILE cc_start: 0.9029 (mm) cc_final: 0.8449 (pt) REVERT: A 319 LEU cc_start: 0.7817 (mt) cc_final: 0.7470 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1294 time to fit residues: 12.9714 Evaluate side-chains 63 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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: 0.6619 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2545 Z= 0.215 Angle : 0.653 7.638 3442 Z= 0.318 Chirality : 0.050 0.148 406 Planarity : 0.004 0.047 430 Dihedral : 4.967 20.641 342 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % 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: -0.69 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.67 (0.45), residues: 115 loop : -1.22 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.029 0.003 PHE A 317 TYR 0.011 0.002 TYR A 40 ARG 0.003 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8406 (m-80) cc_final: 0.8171 (m-10) REVERT: A 33 CYS cc_start: 0.7878 (m) cc_final: 0.7560 (m) REVERT: A 34 GLU cc_start: 0.8535 (tp30) cc_final: 0.7940 (tm-30) REVERT: A 136 LEU cc_start: 0.8925 (mm) cc_final: 0.8351 (mm) REVERT: A 223 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7860 (tppt) REVERT: A 296 ILE cc_start: 0.9082 (mm) cc_final: 0.8633 (pt) REVERT: A 319 LEU cc_start: 0.7737 (mt) cc_final: 0.7418 (mt) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1251 time to fit residues: 12.3858 Evaluate side-chains 65 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 0.0010 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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: 0.6563 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2545 Z= 0.159 Angle : 0.634 7.804 3442 Z= 0.304 Chirality : 0.050 0.161 406 Planarity : 0.003 0.043 430 Dihedral : 4.740 21.791 342 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.60 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 1.44 (0.48), residues: 96 loop : -1.40 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 83 PHE 0.031 0.002 PHE A 317 TYR 0.009 0.001 TYR A 442 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.7464 (m) cc_final: 0.7216 (m) REVERT: A 223 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7544 (tppt) REVERT: A 273 PHE cc_start: 0.7230 (m-80) cc_final: 0.6728 (m-10) REVERT: A 286 ARG cc_start: 0.7893 (tmm-80) cc_final: 0.7568 (tmm-80) REVERT: A 296 ILE cc_start: 0.9033 (mm) cc_final: 0.8591 (pt) REVERT: A 298 PHE cc_start: 0.8165 (m-80) cc_final: 0.7828 (m-10) REVERT: A 319 LEU cc_start: 0.7711 (mt) cc_final: 0.7426 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1315 time to fit residues: 11.8677 Evaluate side-chains 62 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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: 0.6580 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2545 Z= 0.168 Angle : 0.647 8.858 3442 Z= 0.308 Chirality : 0.050 0.175 406 Planarity : 0.003 0.040 430 Dihedral : 4.795 22.110 342 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 1.25 (0.47), residues: 106 loop : -1.43 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 315 PHE 0.029 0.002 PHE A 317 TYR 0.028 0.002 TYR A 442 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.7407 (m) cc_final: 0.7186 (m) REVERT: A 136 LEU cc_start: 0.8722 (mm) cc_final: 0.8189 (mm) REVERT: A 142 SER cc_start: 0.8487 (t) cc_final: 0.8125 (p) REVERT: A 223 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7477 (tppt) REVERT: A 273 PHE cc_start: 0.7219 (m-80) cc_final: 0.6818 (m-10) REVERT: A 296 ILE cc_start: 0.9046 (mm) cc_final: 0.8636 (pt) REVERT: A 298 PHE cc_start: 0.8096 (m-80) cc_final: 0.7727 (m-10) REVERT: A 319 LEU cc_start: 0.7732 (mt) cc_final: 0.7434 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1435 time to fit residues: 13.0847 Evaluate side-chains 61 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.6654 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 2545 Z= 0.267 Angle : 0.704 7.851 3442 Z= 0.342 Chirality : 0.050 0.152 406 Planarity : 0.004 0.040 430 Dihedral : 5.183 21.539 342 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -0.96 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.55 (0.44), residues: 116 loop : -1.48 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 315 PHE 0.017 0.002 PHE A 317 TYR 0.014 0.002 TYR A 442 ARG 0.005 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.7585 (m) cc_final: 0.7117 (m) REVERT: A 96 LEU cc_start: 0.8371 (tt) cc_final: 0.8032 (tt) REVERT: A 136 LEU cc_start: 0.8635 (mm) cc_final: 0.8070 (mm) REVERT: A 137 MET cc_start: 0.5991 (mpp) cc_final: 0.5732 (mpp) REVERT: A 273 PHE cc_start: 0.7367 (m-80) cc_final: 0.7033 (m-10) REVERT: A 296 ILE cc_start: 0.9097 (mm) cc_final: 0.8722 (pt) REVERT: A 298 PHE cc_start: 0.7975 (m-80) cc_final: 0.7543 (m-10) REVERT: A 319 LEU cc_start: 0.7858 (mt) cc_final: 0.7552 (mt) REVERT: A 464 MET cc_start: 0.7644 (mmp) cc_final: 0.7321 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1206 time to fit residues: 11.1782 Evaluate side-chains 60 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.6613 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2545 Z= 0.165 Angle : 0.662 8.367 3442 Z= 0.315 Chirality : 0.049 0.153 406 Planarity : 0.003 0.039 430 Dihedral : 4.893 23.025 342 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.92 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.84 (0.45), residues: 108 loop : -1.55 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 315 PHE 0.012 0.002 PHE A 13 TYR 0.007 0.001 TYR A 116 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8138 (m-80) cc_final: 0.7872 (m-10) REVERT: A 33 CYS cc_start: 0.7382 (m) cc_final: 0.6958 (m) REVERT: A 96 LEU cc_start: 0.8399 (tt) cc_final: 0.8065 (tt) REVERT: A 136 LEU cc_start: 0.8590 (mm) cc_final: 0.8065 (mm) REVERT: A 273 PHE cc_start: 0.7228 (m-80) cc_final: 0.6938 (m-10) REVERT: A 296 ILE cc_start: 0.9077 (mm) cc_final: 0.8669 (pt) REVERT: A 298 PHE cc_start: 0.8028 (m-80) cc_final: 0.7495 (m-10) REVERT: A 319 LEU cc_start: 0.7868 (mt) cc_final: 0.7586 (mt) REVERT: A 492 LEU cc_start: 0.8280 (tp) cc_final: 0.8038 (tp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1270 time to fit residues: 11.9705 Evaluate side-chains 62 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 7 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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: 0.6560 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2545 Z= 0.160 Angle : 0.670 8.452 3442 Z= 0.321 Chirality : 0.050 0.154 406 Planarity : 0.003 0.031 430 Dihedral : 4.719 24.955 342 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.81 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.81 (0.47), residues: 113 loop : -1.45 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.015 0.002 PHE A 317 TYR 0.006 0.001 TYR A 116 ARG 0.005 0.001 ARG A 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.316 Fit side-chains REVERT: A 33 CYS cc_start: 0.6643 (m) cc_final: 0.6331 (m) REVERT: A 136 LEU cc_start: 0.8535 (mm) cc_final: 0.8005 (mm) REVERT: A 137 MET cc_start: 0.6579 (mpp) cc_final: 0.6299 (mtm) REVERT: A 273 PHE cc_start: 0.7209 (m-80) cc_final: 0.6942 (m-10) REVERT: A 281 ILE cc_start: 0.9287 (mm) cc_final: 0.9070 (mm) REVERT: A 296 ILE cc_start: 0.9064 (mm) cc_final: 0.8668 (pt) REVERT: A 298 PHE cc_start: 0.8001 (m-80) cc_final: 0.7530 (m-10) REVERT: A 319 LEU cc_start: 0.7832 (mt) cc_final: 0.7534 (mt) REVERT: A 492 LEU cc_start: 0.8146 (tp) cc_final: 0.7882 (tp) REVERT: A 495 TYR cc_start: 0.5365 (m-80) cc_final: 0.5092 (m-80) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1240 time to fit residues: 11.6795 Evaluate side-chains 59 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 31 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.115845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105179 restraints weight = 6253.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107000 restraints weight = 4259.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108430 restraints weight = 3169.044| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2545 Z= 0.177 Angle : 0.667 8.567 3442 Z= 0.320 Chirality : 0.050 0.166 406 Planarity : 0.003 0.037 430 Dihedral : 4.799 24.187 342 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.73 (0.47), residues: 113 loop : -1.44 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 315 PHE 0.014 0.002 PHE A 13 TYR 0.025 0.001 TYR A 47 ARG 0.007 0.001 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.65 seconds wall clock time: 20 minutes 54.57 seconds (1254.57 seconds total)