Starting phenix.real_space_refine on Tue Feb 11 07:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_15411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_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/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_15411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_15411.map" model { file = "/net/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_15411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afx_15411/02_2025/8afx_15411.cif" } 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. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.21, per 1000 atoms: 0.88 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 237.3 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: 0.66 Time building geometry restraints manager: 0.63 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: 0.00 - 3.35: 3411 3.35 - 6.71: 22 6.71 - 10.06: 7 10.06 - 13.41: 1 13.41 - 16.76: 1 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 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OD1 ASN A 79 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 101 " pdb=" N SER A 103 " model vdw 2.234 3.120 nonbonded pdb=" OG SER A 44 " pdb=" OH TYR A 47 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" N GLY A 17 " model vdw 2.238 3.120 ... (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: 0.930 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.267 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.1173 time to fit residues: 10.3729 Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 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: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.116505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.105516 restraints weight = 6075.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107215 restraints weight = 4283.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.108478 restraints weight = 3259.791| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2545 Z= 0.251 Angle : 0.658 6.968 3442 Z= 0.337 Chirality : 0.050 0.158 406 Planarity : 0.005 0.057 430 Dihedral : 5.401 18.882 342 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: -0.53 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.98 (0.43), residues: 122 loop : -1.36 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 315 PHE 0.011 0.002 PHE A 39 TYR 0.010 0.001 TYR A 116 ARG 0.005 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 81 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.318 Fit side-chains REVERT: A 58 LEU cc_start: 0.9158 (tp) cc_final: 0.8907 (tp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1209 time to fit residues: 11.9737 Evaluate side-chains 59 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108367 restraints weight = 6302.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110004 restraints weight = 4430.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111251 restraints weight = 3383.691| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2545 Z= 0.267 Angle : 0.683 7.384 3442 Z= 0.345 Chirality : 0.051 0.149 406 Planarity : 0.004 0.035 430 Dihedral : 5.476 18.891 342 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: -0.97 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.42 (0.42), residues: 127 loop : -1.49 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 244 PHE 0.015 0.003 PHE A 317 TYR 0.027 0.002 TYR A 47 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 76 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.476 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1236 time to fit residues: 11.4026 Evaluate side-chains 56 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 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 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.113912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103461 restraints weight = 6273.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.105182 restraints weight = 4365.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.106449 restraints weight = 3293.387| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2545 Z= 0.228 Angle : 0.654 7.148 3442 Z= 0.331 Chirality : 0.051 0.146 406 Planarity : 0.004 0.032 430 Dihedral : 5.438 20.479 342 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: -1.14 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.40 (0.43), residues: 122 loop : -1.65 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.024 0.003 PHE A 13 TYR 0.024 0.002 TYR A 47 ARG 0.002 0.000 ARG A 485 *********************** 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 79 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 28 PHE cc_start: 0.8581 (p90) cc_final: 0.8309 (p90) REVERT: A 33 CYS cc_start: 0.8435 (m) cc_final: 0.8129 (m) REVERT: A 75 LEU cc_start: 0.8956 (tt) cc_final: 0.8678 (tt) REVERT: A 223 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8695 (tppt) REVERT: A 298 PHE cc_start: 0.8857 (m-80) cc_final: 0.8402 (m-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1405 time to fit residues: 13.3161 Evaluate side-chains 61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.108531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097728 restraints weight = 6276.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.099592 restraints weight = 4224.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100999 restraints weight = 3085.715| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3270 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= 0.202 Angle : 0.654 7.403 3442 Z= 0.329 Chirality : 0.052 0.186 406 Planarity : 0.004 0.045 430 Dihedral : 5.323 20.609 342 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -1.09 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.74 (0.44), residues: 111 loop : -1.71 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.020 0.002 PHE A 13 TYR 0.020 0.002 TYR A 47 ARG 0.002 0.000 ARG A 134 *********************** 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 78 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.8316 (m) cc_final: 0.7890 (m) REVERT: A 34 GLU cc_start: 0.8878 (tp30) cc_final: 0.8105 (tm-30) REVERT: A 273 PHE cc_start: 0.8000 (m-80) cc_final: 0.7630 (m-10) REVERT: A 296 ILE cc_start: 0.9226 (mm) cc_final: 0.8533 (pt) REVERT: A 298 PHE cc_start: 0.8860 (m-80) cc_final: 0.8482 (m-10) REVERT: A 319 LEU cc_start: 0.8982 (mt) cc_final: 0.8764 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1198 time to fit residues: 11.3823 Evaluate side-chains 57 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.116498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.106098 restraints weight = 6196.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107744 restraints weight = 4367.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108953 restraints weight = 3318.301| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2545 Z= 0.272 Angle : 0.692 7.861 3442 Z= 0.349 Chirality : 0.052 0.193 406 Planarity : 0.004 0.020 430 Dihedral : 5.491 20.952 342 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.28 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.50 (0.44), residues: 116 loop : -1.83 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 244 PHE 0.014 0.002 PHE A 317 TYR 0.020 0.002 TYR A 47 ARG 0.004 0.001 ARG A 134 *********************** 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 79 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.282 Fit side-chains REVERT: A 28 PHE cc_start: 0.8640 (p90) cc_final: 0.8390 (p90) REVERT: A 33 CYS cc_start: 0.8326 (m) cc_final: 0.7860 (m) REVERT: A 34 GLU cc_start: 0.8989 (tp30) cc_final: 0.8217 (tm-30) REVERT: A 47 TYR cc_start: 0.8531 (m-10) cc_final: 0.8195 (m-10) REVERT: A 75 LEU cc_start: 0.8889 (tt) cc_final: 0.8673 (tt) REVERT: A 96 LEU cc_start: 0.8163 (tt) cc_final: 0.7954 (tt) REVERT: A 136 LEU cc_start: 0.8958 (mm) cc_final: 0.8648 (mm) REVERT: A 273 PHE cc_start: 0.8062 (m-80) cc_final: 0.7477 (m-10) REVERT: A 296 ILE cc_start: 0.9330 (mm) cc_final: 0.8668 (pt) REVERT: A 298 PHE cc_start: 0.8869 (m-80) cc_final: 0.8557 (m-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1147 time to fit residues: 11.2620 Evaluate side-chains 60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.109146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098224 restraints weight = 6464.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.100081 restraints weight = 4406.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.101501 restraints weight = 3223.417| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2545 Z= 0.177 Angle : 0.651 8.178 3442 Z= 0.322 Chirality : 0.051 0.188 406 Planarity : 0.003 0.019 430 Dihedral : 5.171 22.395 342 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.18 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.79 (0.46), residues: 106 loop : -1.79 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.021 0.002 PHE A 39 TYR 0.018 0.002 TYR A 47 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 74 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 33 CYS cc_start: 0.7652 (m) cc_final: 0.7199 (m) REVERT: A 34 GLU cc_start: 0.8976 (tp30) cc_final: 0.8093 (tm-30) REVERT: A 136 LEU cc_start: 0.8951 (mm) cc_final: 0.8663 (mm) REVERT: A 273 PHE cc_start: 0.8028 (m-80) cc_final: 0.7080 (m-10) REVERT: A 296 ILE cc_start: 0.9246 (mm) cc_final: 0.8590 (pt) REVERT: A 298 PHE cc_start: 0.8819 (m-80) cc_final: 0.8523 (m-10) REVERT: A 319 LEU cc_start: 0.8914 (mt) cc_final: 0.8672 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1257 time to fit residues: 11.3018 Evaluate side-chains 59 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.115465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104457 restraints weight = 6220.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.106364 restraints weight = 4203.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.107778 restraints weight = 3080.454| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3775 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 : 0.666 8.302 3442 Z= 0.328 Chirality : 0.051 0.196 406 Planarity : 0.003 0.019 430 Dihedral : 5.190 23.329 342 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -1.18 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.71 (0.45), residues: 116 loop : -1.86 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.019 0.002 PHE A 39 TYR 0.028 0.002 TYR A 40 ARG 0.003 0.000 ARG A 286 *********************** 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 74 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.267 Fit side-chains REVERT: A 33 CYS cc_start: 0.7892 (m) cc_final: 0.7380 (m) REVERT: A 34 GLU cc_start: 0.8996 (tp30) cc_final: 0.8172 (tm-30) REVERT: A 136 LEU cc_start: 0.8927 (mm) cc_final: 0.8594 (mm) REVERT: A 273 PHE cc_start: 0.8019 (m-80) cc_final: 0.7190 (m-10) REVERT: A 296 ILE cc_start: 0.9231 (mm) cc_final: 0.8568 (pt) REVERT: A 298 PHE cc_start: 0.8756 (m-80) cc_final: 0.8485 (m-10) REVERT: A 319 LEU cc_start: 0.8914 (mt) cc_final: 0.8687 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1307 time to fit residues: 11.8183 Evaluate side-chains 60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.119718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109184 restraints weight = 6045.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.110980 restraints weight = 4160.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112370 restraints weight = 3072.289| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3813 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= 0.177 Angle : 0.683 8.743 3442 Z= 0.331 Chirality : 0.051 0.187 406 Planarity : 0.003 0.019 430 Dihedral : 5.165 24.072 342 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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: -1.18 (0.43), residues: 311 helix: None (None), residues: 0 sheet: 0.86 (0.45), residues: 111 loop : -1.91 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 315 PHE 0.017 0.002 PHE A 39 TYR 0.015 0.001 TYR A 40 ARG 0.004 0.000 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 73 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.277 Fit side-chains REVERT: A 33 CYS cc_start: 0.7714 (m) cc_final: 0.7327 (m) REVERT: A 34 GLU cc_start: 0.9046 (tp30) cc_final: 0.8269 (tm-30) REVERT: A 36 PHE cc_start: 0.7339 (t80) cc_final: 0.7117 (t80) REVERT: A 136 LEU cc_start: 0.8670 (mm) cc_final: 0.8392 (mm) REVERT: A 273 PHE cc_start: 0.7906 (m-80) cc_final: 0.7134 (m-10) REVERT: A 296 ILE cc_start: 0.9179 (mm) cc_final: 0.8584 (pt) REVERT: A 298 PHE cc_start: 0.8769 (m-80) cc_final: 0.8449 (m-10) REVERT: A 319 LEU cc_start: 0.8949 (mt) cc_final: 0.8699 (mt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1204 time to fit residues: 10.8163 Evaluate side-chains 58 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 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 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 13 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.112032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.101196 restraints weight = 6202.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.103204 restraints weight = 4147.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104665 restraints weight = 2987.344| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3912 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= 0.179 Angle : 0.687 8.687 3442 Z= 0.332 Chirality : 0.051 0.187 406 Planarity : 0.003 0.023 430 Dihedral : 5.181 25.071 342 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -1.22 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.56 (0.44), residues: 125 loop : -1.91 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 315 PHE 0.018 0.002 PHE A 39 TYR 0.011 0.001 TYR A 40 ARG 0.004 0.000 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 72 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.311 Fit side-chains REVERT: A 33 CYS cc_start: 0.7747 (m) cc_final: 0.7448 (m) REVERT: A 34 GLU cc_start: 0.9055 (tp30) cc_final: 0.8306 (tm-30) REVERT: A 77 ILE cc_start: 0.8868 (mp) cc_final: 0.8647 (mt) REVERT: A 139 MET cc_start: 0.6168 (ptm) cc_final: 0.5959 (ptt) REVERT: A 273 PHE cc_start: 0.7832 (m-80) cc_final: 0.6977 (m-10) REVERT: A 296 ILE cc_start: 0.9188 (mm) cc_final: 0.8570 (pt) REVERT: A 298 PHE cc_start: 0.8756 (m-80) cc_final: 0.8490 (m-10) REVERT: A 319 LEU cc_start: 0.8953 (mt) cc_final: 0.8695 (mt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1235 time to fit residues: 10.8816 Evaluate side-chains 58 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.116326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.105594 restraints weight = 6133.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.107429 restraints weight = 4212.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108843 restraints weight = 3127.104| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4020 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= 0.163 Angle : 0.659 8.709 3442 Z= 0.318 Chirality : 0.050 0.185 406 Planarity : 0.003 0.038 430 Dihedral : 5.083 24.475 342 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -1.10 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.76 (0.44), residues: 123 loop : -1.91 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 315 PHE 0.018 0.002 PHE A 39 TYR 0.010 0.001 TYR A 40 ARG 0.002 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1227.37 seconds wall clock time: 22 minutes 33.79 seconds (1353.79 seconds total)