Starting phenix.real_space_refine on Fri Aug 22 13:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.map" model { file = "/net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p4z_71290/08_2025/9p4z_71290.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.011 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 Na 2 4.78 5 C 2095 2.51 5 N 492 2.21 5 O 556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3167 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3098 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {' NA': 2, '9Z9': 1, 'CLR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 0.78, per 1000 atoms: 0.25 Number of scatterers: 3167 At special positions: 0 Unit cell: (73.87, 65.57, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 Na 2 11.00 O 556 8.00 N 492 7.00 C 2095 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: 0.21 Conformation dependent library (CDL) restraints added in 70.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 85.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 19 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.645A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 86 removed outlier: 3.516A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.604A pdb=" N VAL A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.685A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 276 through 299 removed outlier: 4.113A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.706A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.549A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.645A pdb=" N SER A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 414 through 426 removed outlier: 4.002A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 466 removed outlier: 4.250A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 242 hydrogen bonds defined for protein. 720 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: 0.30 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 964 1.34 - 1.46: 684 1.46 - 1.58: 1530 1.58 - 1.70: 2 1.70 - 1.81: 39 Bond restraints: 3219 Sorted by residual: bond pdb=" N ASP A 440 " pdb=" CA ASP A 440 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.28e+00 bond pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.17e-02 7.31e+03 5.04e+00 bond pdb=" C6 CLR A 604 " pdb=" C7 CLR A 604 " ideal model delta sigma weight residual 1.492 1.533 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C20 CLR A 604 " pdb=" C22 CLR A 604 " ideal model delta sigma weight residual 1.535 1.576 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C23 9Z9 A 603 " pdb=" C24 9Z9 A 603 " ideal model delta sigma weight residual 1.524 1.564 -0.040 2.00e-02 2.50e+03 3.99e+00 ... (remaining 3214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4271 1.63 - 3.26: 81 3.26 - 4.89: 23 4.89 - 6.52: 5 6.52 - 8.15: 3 Bond angle restraints: 4383 Sorted by residual: angle pdb=" CA ASP A 440 " pdb=" CB ASP A 440 " pdb=" CG ASP A 440 " ideal model delta sigma weight residual 112.60 116.55 -3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA VAL A 358 " pdb=" C VAL A 358 " pdb=" O VAL A 358 " ideal model delta sigma weight residual 121.17 117.89 3.28 1.06e+00 8.90e-01 9.55e+00 angle pdb=" O72 9Z9 A 603 " pdb=" C73 9Z9 A 603 " pdb=" O80 9Z9 A 603 " ideal model delta sigma weight residual 110.27 102.12 8.15 3.00e+00 1.11e-01 7.38e+00 angle pdb=" CA ASP A 440 " pdb=" C ASP A 440 " pdb=" O ASP A 440 " ideal model delta sigma weight residual 120.82 118.10 2.72 1.05e+00 9.07e-01 6.73e+00 angle pdb=" C22 CLR A 604 " pdb=" C23 CLR A 604 " pdb=" C24 CLR A 604 " ideal model delta sigma weight residual 111.95 104.26 7.69 3.00e+00 1.11e-01 6.58e+00 ... (remaining 4378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.11: 1913 27.11 - 54.22: 107 54.22 - 81.33: 14 81.33 - 108.44: 1 108.44 - 135.55: 4 Dihedral angle restraints: 2039 sinusoidal: 873 harmonic: 1166 Sorted by residual: dihedral pdb=" C16 9Z9 A 603 " pdb=" C17 9Z9 A 603 " pdb=" O20 9Z9 A 603 " pdb=" C21 9Z9 A 603 " ideal model delta sinusoidal sigma weight residual -75.05 60.50 -135.55 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C18 9Z9 A 603 " pdb=" C17 9Z9 A 603 " pdb=" O20 9Z9 A 603 " pdb=" C21 9Z9 A 603 " ideal model delta sinusoidal sigma weight residual 163.81 -60.69 -135.50 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C22 9Z9 A 603 " pdb=" C23 9Z9 A 603 " pdb=" C48 9Z9 A 603 " pdb=" O49 9Z9 A 603 " ideal model delta sinusoidal sigma weight residual 177.15 -69.39 -113.46 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 2036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 522 0.074 - 0.149: 35 0.149 - 0.223: 2 0.223 - 0.298: 1 0.298 - 0.372: 3 Chirality restraints: 563 Sorted by residual: chirality pdb=" C17 CLR A 604 " pdb=" C13 CLR A 604 " pdb=" C16 CLR A 604 " pdb=" C20 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C20 CLR A 604 " pdb=" C17 CLR A 604 " pdb=" C21 CLR A 604 " pdb=" C22 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C13 CLR A 604 " pdb=" C12 CLR A 604 " pdb=" C14 CLR A 604 " pdb=" C17 CLR A 604 " both_signs ideal model delta sigma weight residual False -2.93 -3.24 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 560 not shown) Planarity restraints: 517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 358 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.56e+00 pdb=" C VAL A 358 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL A 358 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 359 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 428 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 429 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 391 " -0.005 2.00e-02 2.50e+03 9.53e-03 9.07e-01 pdb=" C ILE A 391 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 391 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 392 " -0.006 2.00e-02 2.50e+03 ... (remaining 514 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 27 2.61 - 3.18: 2977 3.18 - 3.75: 4827 3.75 - 4.33: 6956 4.33 - 4.90: 11272 Nonbonded interactions: 26059 Sorted by model distance: nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.034 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 602 " model vdw 2.076 2.470 nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 602 " model vdw 2.166 2.470 nonbonded pdb=" OD1 ASP A 455 " pdb="NA NA A 601 " model vdw 2.189 2.470 nonbonded pdb=" O ASN A 451 " pdb="NA NA A 601 " model vdw 2.196 2.470 ... (remaining 26054 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.460 Find NCS groups from input model: 0.000 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.004 0.041 3219 Z= 0.186 Angle : 0.617 8.148 4383 Z= 0.301 Chirality : 0.047 0.372 563 Planarity : 0.003 0.038 517 Dihedral : 16.921 135.546 1287 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 21.99 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.43), residues: 401 helix: 1.25 (0.30), residues: 322 sheet: -0.77 (1.22), residues: 18 loop : -1.32 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.007 0.001 TYR A 97 PHE 0.007 0.001 PHE A 341 TRP 0.010 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3219) covalent geometry : angle 0.61702 ( 4383) hydrogen bonds : bond 0.22445 ( 242) hydrogen bonds : angle 7.52963 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.075 Fit side-chains REVERT: A 161 GLN cc_start: 0.8682 (mt0) cc_final: 0.8403 (mt0) REVERT: A 440 ASP cc_start: 0.6807 (t0) cc_final: 0.6359 (p0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.4452 time to fit residues: 21.0217 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.190253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153921 restraints weight = 3727.076| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.46 r_work: 0.3618 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3219 Z= 0.135 Angle : 0.547 5.544 4383 Z= 0.283 Chirality : 0.039 0.183 563 Planarity : 0.004 0.040 517 Dihedral : 9.964 116.370 587 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.81 % Allowed : 18.48 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.42), residues: 401 helix: 1.85 (0.28), residues: 329 sheet: -0.98 (1.17), residues: 18 loop : -1.03 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 353 TYR 0.013 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.013 0.001 TRP A 441 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3219) covalent geometry : angle 0.54693 ( 4383) hydrogen bonds : bond 0.04851 ( 242) hydrogen bonds : angle 4.40605 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.115 Fit side-chains REVERT: A 161 GLN cc_start: 0.8702 (mt0) cc_final: 0.8476 (mt0) REVERT: A 346 GLU cc_start: 0.6717 (tp30) cc_final: 0.6498 (tt0) REVERT: A 440 ASP cc_start: 0.6563 (t0) cc_final: 0.6133 (p0) outliers start: 13 outliers final: 4 residues processed: 59 average time/residue: 0.3271 time to fit residues: 20.0173 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154886 restraints weight = 3736.095| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.40 r_work: 0.3615 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3219 Z= 0.169 Angle : 0.569 6.621 4383 Z= 0.294 Chirality : 0.040 0.155 563 Planarity : 0.004 0.045 517 Dihedral : 8.995 106.873 587 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.40 % Allowed : 18.18 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.42), residues: 401 helix: 1.75 (0.28), residues: 328 sheet: -1.14 (1.15), residues: 18 loop : -1.14 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 353 TYR 0.012 0.002 TYR A 97 PHE 0.012 0.002 PHE A 218 TRP 0.008 0.001 TRP A 441 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3219) covalent geometry : angle 0.56866 ( 4383) hydrogen bonds : bond 0.05046 ( 242) hydrogen bonds : angle 4.35994 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.070 Fit side-chains REVERT: A 161 GLN cc_start: 0.8751 (mt0) cc_final: 0.8489 (mt0) REVERT: A 356 ARG cc_start: 0.6897 (mtp-110) cc_final: 0.6674 (ppt170) REVERT: A 440 ASP cc_start: 0.6536 (t0) cc_final: 0.6204 (p0) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.3740 time to fit residues: 23.4894 Evaluate side-chains 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.187549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153878 restraints weight = 3794.546| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.44 r_work: 0.3407 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3219 Z= 0.192 Angle : 0.596 8.009 4383 Z= 0.305 Chirality : 0.041 0.170 563 Planarity : 0.004 0.046 517 Dihedral : 8.327 99.371 587 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.52 % Allowed : 20.53 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.41), residues: 401 helix: 1.50 (0.28), residues: 325 sheet: -1.36 (1.15), residues: 18 loop : -0.98 (0.74), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 353 TYR 0.016 0.002 TYR A 97 PHE 0.013 0.002 PHE A 218 TRP 0.007 0.001 TRP A 441 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 3219) covalent geometry : angle 0.59587 ( 4383) hydrogen bonds : bond 0.05097 ( 242) hydrogen bonds : angle 4.38705 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.087 Fit side-chains REVERT: A 161 GLN cc_start: 0.8696 (mt0) cc_final: 0.8369 (mt0) REVERT: A 440 ASP cc_start: 0.6594 (t0) cc_final: 0.6103 (p0) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.4044 time to fit residues: 24.1832 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.190187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154544 restraints weight = 3794.118| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.38 r_work: 0.3453 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3219 Z= 0.134 Angle : 0.527 6.515 4383 Z= 0.270 Chirality : 0.039 0.151 563 Planarity : 0.004 0.044 517 Dihedral : 7.536 93.211 587 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.11 % Allowed : 21.41 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.42), residues: 401 helix: 1.76 (0.28), residues: 328 sheet: -1.30 (1.20), residues: 18 loop : -0.98 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.016 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.006 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3219) covalent geometry : angle 0.52650 ( 4383) hydrogen bonds : bond 0.04326 ( 242) hydrogen bonds : angle 4.11320 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.099 Fit side-chains REVERT: A 39 ARG cc_start: 0.7891 (ptm-80) cc_final: 0.7601 (ptm160) REVERT: A 161 GLN cc_start: 0.8640 (mt0) cc_final: 0.8369 (mt0) REVERT: A 440 ASP cc_start: 0.6484 (t0) cc_final: 0.5981 (p0) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.3712 time to fit residues: 22.6287 Evaluate side-chains 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 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 = 0.4040 r_free = 0.4040 target = 0.182593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144823 restraints weight = 3616.703| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.38 r_work: 0.3442 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3219 Z= 0.144 Angle : 0.536 7.174 4383 Z= 0.273 Chirality : 0.039 0.146 563 Planarity : 0.004 0.041 517 Dihedral : 7.393 90.436 587 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.81 % Allowed : 21.99 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.42), residues: 401 helix: 1.78 (0.28), residues: 328 sheet: -1.16 (1.22), residues: 18 loop : -0.98 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.014 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.005 0.001 TRP A 441 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3219) covalent geometry : angle 0.53598 ( 4383) hydrogen bonds : bond 0.04425 ( 242) hydrogen bonds : angle 4.10958 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.075 Fit side-chains REVERT: A 161 GLN cc_start: 0.8670 (mt0) cc_final: 0.8394 (mt0) REVERT: A 440 ASP cc_start: 0.6531 (t0) cc_final: 0.6069 (p0) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.4673 time to fit residues: 27.8656 Evaluate side-chains 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.184241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148266 restraints weight = 3645.680| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.75 r_work: 0.3454 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.035 3219 Z= 0.131 Angle : 0.535 7.031 4383 Z= 0.274 Chirality : 0.039 0.153 563 Planarity : 0.004 0.040 517 Dihedral : 7.208 87.587 587 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.11 % Allowed : 20.82 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.42), residues: 401 helix: 1.87 (0.28), residues: 330 sheet: -1.04 (1.23), residues: 18 loop : -0.92 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.013 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.005 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3219) covalent geometry : angle 0.53454 ( 4383) hydrogen bonds : bond 0.04169 ( 242) hydrogen bonds : angle 3.98433 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.123 Fit side-chains REVERT: A 39 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.7589 (ptm160) REVERT: A 161 GLN cc_start: 0.8673 (mt0) cc_final: 0.8424 (mt0) REVERT: A 315 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5175 (mmt90) REVERT: A 432 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: A 440 ASP cc_start: 0.6429 (t0) cc_final: 0.6017 (p0) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 0.4114 time to fit residues: 24.6523 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.184359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149195 restraints weight = 3696.408| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.68 r_work: 0.3510 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3219 Z= 0.133 Angle : 0.535 7.300 4383 Z= 0.274 Chirality : 0.038 0.124 563 Planarity : 0.004 0.040 517 Dihedral : 6.987 83.892 587 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.40 % Allowed : 21.70 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.42), residues: 401 helix: 1.85 (0.28), residues: 330 sheet: -1.01 (1.23), residues: 18 loop : -0.96 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.020 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.005 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3219) covalent geometry : angle 0.53545 ( 4383) hydrogen bonds : bond 0.04218 ( 242) hydrogen bonds : angle 4.06939 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.121 Fit side-chains REVERT: A 39 ARG cc_start: 0.7979 (ptm-80) cc_final: 0.7682 (ptm160) REVERT: A 161 GLN cc_start: 0.8696 (mt0) cc_final: 0.8452 (mt0) REVERT: A 322 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6345 (mm-40) REVERT: A 432 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: A 440 ASP cc_start: 0.6420 (t0) cc_final: 0.6205 (p0) REVERT: A 455 ASP cc_start: 0.6399 (m-30) cc_final: 0.6140 (m-30) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.3627 time to fit residues: 22.1733 Evaluate side-chains 59 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.182170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146281 restraints weight = 3645.262| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.64 r_work: 0.3450 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3219 Z= 0.144 Angle : 0.549 7.658 4383 Z= 0.280 Chirality : 0.040 0.167 563 Planarity : 0.004 0.040 517 Dihedral : 6.883 81.313 587 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.52 % Allowed : 22.87 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.42), residues: 401 helix: 1.78 (0.28), residues: 330 sheet: -0.98 (1.24), residues: 18 loop : -0.90 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.028 0.002 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.008 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3219) covalent geometry : angle 0.54867 ( 4383) hydrogen bonds : bond 0.04336 ( 242) hydrogen bonds : angle 4.08557 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.077 Fit side-chains REVERT: A 39 ARG cc_start: 0.7921 (ptm-80) cc_final: 0.7620 (ptm160) REVERT: A 161 GLN cc_start: 0.8670 (mt0) cc_final: 0.8408 (mt0) REVERT: A 322 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6354 (mm-40) REVERT: A 432 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: A 440 ASP cc_start: 0.6476 (t0) cc_final: 0.6175 (p0) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.3643 time to fit residues: 21.8363 Evaluate side-chains 60 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.184827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149835 restraints weight = 3657.646| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.70 r_work: 0.3464 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3219 Z= 0.131 Angle : 0.542 8.580 4383 Z= 0.274 Chirality : 0.039 0.149 563 Planarity : 0.004 0.040 517 Dihedral : 6.597 76.549 587 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.93 % Allowed : 23.75 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.42), residues: 401 helix: 1.82 (0.28), residues: 331 sheet: -0.90 (1.25), residues: 18 loop : -0.80 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.024 0.001 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.008 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3219) covalent geometry : angle 0.54184 ( 4383) hydrogen bonds : bond 0.04144 ( 242) hydrogen bonds : angle 4.07504 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.072 Fit side-chains REVERT: A 161 GLN cc_start: 0.8664 (mt0) cc_final: 0.8404 (mt0) REVERT: A 432 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: A 440 ASP cc_start: 0.6473 (t0) cc_final: 0.6210 (p0) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.3998 time to fit residues: 23.5591 Evaluate side-chains 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.183200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147985 restraints weight = 3712.824| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.69 r_work: 0.3429 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3219 Z= 0.147 Angle : 0.561 8.568 4383 Z= 0.284 Chirality : 0.039 0.148 563 Planarity : 0.004 0.040 517 Dihedral : 6.310 68.482 587 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.81 % Allowed : 23.17 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.42), residues: 401 helix: 1.75 (0.28), residues: 330 sheet: -0.92 (1.26), residues: 18 loop : -0.82 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.024 0.002 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.009 0.001 TRP A 441 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3219) covalent geometry : angle 0.56150 ( 4383) hydrogen bonds : bond 0.04361 ( 242) hydrogen bonds : angle 4.12588 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1188.65 seconds wall clock time: 20 minutes 56.78 seconds (1256.78 seconds total)