Starting phenix.real_space_refine on Wed Jul 1 22:00:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_71290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_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 { model { file = "/net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_71290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_71290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_71290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p4z_71290/07_2026/9p4z_71290.map" } 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-dev-6108/lib/python3.11/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, 67 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'9Z9': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Time building chain proxies: 1.08, per 1000 atoms: 0.34 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: 0.38 Conformation dependent library (CDL) restraints added in 146.7 milliseconds 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: 0.10 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: 0.49 Time building geometry restraints manager: 0.47 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 3.210 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 602 " model vdw 2.076 3.210 nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 602 " model vdw 2.166 3.210 nonbonded pdb=" OD1 ASP A 455 " pdb="NA NA A 601 " model vdw 2.189 3.210 nonbonded pdb=" O ASN A 451 " pdb="NA NA A 601 " model vdw 2.196 3.210 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 5.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 are 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/Z covalent geometry : bond 0.00385 / 0.19 ( 3219) covalent geometry : angle 0.61702 / 0.30 ( 4383) hydrogen bonds : bond 0.22445 / 15.37 ( 242) hydrogen bonds : angle 7.52963 / 5.37 ( 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 : 0.116 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: 0.5637 time to fit residues: 26.6704 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 : 0.116 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4122 r_free = 0.4122 target = 0.189641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152975 restraints weight = 3734.249| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.48 r_work: 0.3611 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3219 Z= 0.144 Angle : 0.562 5.514 4383 Z= 0.293 Chirality : 0.040 0.183 563 Planarity : 0.004 0.040 517 Dihedral : 10.081 116.864 587 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.11 % Allowed : 19.06 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.42), residues: 401 helix: 1.82 (0.28), residues: 329 sheet: -0.98 (1.17), residues: 18 loop : -1.05 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 353 TYR 0.012 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.012 0.001 TRP A 441 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 3219) covalent geometry : angle 0.56223 / 0.29 ( 4383) hydrogen bonds : bond 0.05079 / 3.41 ( 242) hydrogen bonds : angle 4.45438 / 3.16 ( 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 68 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.126 Fit side-chains REVERT: A 161 GLN cc_start: 0.8719 (mt0) cc_final: 0.8478 (mt0) REVERT: A 440 ASP cc_start: 0.6638 (t0) cc_final: 0.6198 (p0) outliers start: 14 outliers final: 4 residues processed: 62 average time/residue: 0.4470 time to fit residues: 28.7103 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 : 0.154 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153569 restraints weight = 3704.911| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.40 r_work: 0.3450 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2260 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= 0.135 Angle : 0.536 6.779 4383 Z= 0.278 Chirality : 0.039 0.138 563 Planarity : 0.004 0.044 517 Dihedral : 8.768 106.531 587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.69 % Allowed : 19.35 % 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 are not related in a simple way. whole: 2.03 (0.42), residues: 401 helix: 1.84 (0.28), residues: 332 sheet: -1.00 (1.18), residues: 18 loop : -0.99 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.017 0.001 TYR A 97 PHE 0.010 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/Z covalent geometry : bond 0.00307 / 0.13 ( 3219) covalent geometry : angle 0.53625 / 0.28 ( 4383) hydrogen bonds : bond 0.04672 / 3.11 ( 242) hydrogen bonds : angle 4.23773 / 3.02 ( 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 68 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.072 Fit side-chains REVERT: A 161 GLN cc_start: 0.8632 (mt0) cc_final: 0.8370 (mt0) REVERT: A 356 ARG cc_start: 0.6802 (mtp-110) cc_final: 0.6583 (ppt170) REVERT: A 440 ASP cc_start: 0.6465 (t0) cc_final: 0.5930 (p0) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.4135 time to fit residues: 26.1325 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 : 0.118 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155067 restraints weight = 3779.431| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.39 r_work: 0.3626 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2556 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= 0.138 Angle : 0.534 6.676 4383 Z= 0.275 Chirality : 0.039 0.147 563 Planarity : 0.004 0.043 517 Dihedral : 7.679 95.349 587 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.81 % Allowed : 20.53 % Favored : 75.66 % 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 are not related in a simple way. whole: 2.00 (0.42), residues: 401 helix: 1.83 (0.28), residues: 332 sheet: -1.03 (1.18), residues: 18 loop : -1.01 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.014 0.001 TYR A 97 PHE 0.011 0.001 PHE A 218 TRP 0.007 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3219) covalent geometry : angle 0.53406 / 0.27 ( 4383) hydrogen bonds : bond 0.04450 / 2.98 ( 242) hydrogen bonds : angle 4.16940 / 2.98 ( 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.134 Fit side-chains REVERT: A 39 ARG cc_start: 0.8133 (ptm-80) cc_final: 0.7757 (ptm160) REVERT: A 161 GLN cc_start: 0.8720 (mt0) cc_final: 0.8493 (mt0) REVERT: A 431 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: A 440 ASP cc_start: 0.6433 (t0) cc_final: 0.6182 (p0) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.4461 time to fit residues: 26.2861 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 : 0.119 ------------------------------------------------------------------------------- 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 322 GLN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 431 GLU 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: 0.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153849 restraints weight = 3753.177| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.38 r_work: 0.3532 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3219 Z= 0.148 Angle : 0.543 6.904 4383 Z= 0.277 Chirality : 0.039 0.147 563 Planarity : 0.004 0.045 517 Dihedral : 7.322 90.397 587 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.11 % Allowed : 21.11 % Favored : 74.78 % 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 are not related in a simple way. whole: 1.95 (0.42), residues: 401 helix: 1.79 (0.28), residues: 332 sheet: -1.08 (1.20), residues: 18 loop : -0.94 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 353 TYR 0.011 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/Z covalent geometry : bond 0.00354 / 0.15 ( 3219) covalent geometry : angle 0.54266 / 0.28 ( 4383) hydrogen bonds : bond 0.04528 / 3.04 ( 242) hydrogen bonds : angle 4.13265 / 2.96 ( 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 66 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.073 Fit side-chains REVERT: A 39 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7828 (ptm160) REVERT: A 161 GLN cc_start: 0.8700 (mt0) cc_final: 0.8463 (mt0) REVERT: A 353 ARG cc_start: 0.5873 (ptp-110) cc_final: 0.5496 (mtm180) REVERT: A 431 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6763 (tp30) REVERT: A 440 ASP cc_start: 0.6556 (t0) cc_final: 0.6237 (p0) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.4586 time to fit residues: 29.3267 Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU 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 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 431 GLU 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: 6.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.190071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154409 restraints weight = 3778.837| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.37 r_work: 0.3614 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3219 Z= 0.149 Angle : 0.554 7.484 4383 Z= 0.282 Chirality : 0.039 0.159 563 Planarity : 0.004 0.041 517 Dihedral : 7.231 87.874 587 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 are not related in a simple way. whole: 1.97 (0.42), residues: 401 helix: 1.81 (0.28), residues: 328 sheet: -1.13 (1.20), residues: 18 loop : -0.76 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 353 TYR 0.011 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/Z covalent geometry : bond 0.00352 / 0.15 ( 3219) covalent geometry : angle 0.55419 / 0.28 ( 4383) hydrogen bonds : bond 0.04448 / 2.97 ( 242) hydrogen bonds : angle 4.08858 / 2.93 ( 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 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.072 Fit side-chains REVERT: A 39 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7866 (ptm160) REVERT: A 161 GLN cc_start: 0.8696 (mt0) cc_final: 0.8455 (mt0) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.4329 time to fit residues: 25.4113 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.184542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149912 restraints weight = 3692.201| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.74 r_work: 0.3453 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3196 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= 0.136 Angle : 0.547 7.084 4383 Z= 0.279 Chirality : 0.038 0.124 563 Planarity : 0.004 0.040 517 Dihedral : 6.976 83.742 587 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.11 % Allowed : 21.99 % 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 are not related in a simple way. whole: 2.09 (0.43), residues: 401 helix: 1.86 (0.28), residues: 330 sheet: -1.10 (1.22), residues: 18 loop : -0.54 (0.91), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 353 TYR 0.017 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/Z covalent geometry : bond 0.00313 / 0.14 ( 3219) covalent geometry : angle 0.54691 / 0.28 ( 4383) hydrogen bonds : bond 0.04283 / 2.87 ( 242) hydrogen bonds : angle 4.03532 / 2.89 ( 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 63 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.107 Fit side-chains REVERT: A 39 ARG cc_start: 0.8012 (ptm-80) cc_final: 0.7635 (ptm160) REVERT: A 161 GLN cc_start: 0.8681 (mt0) cc_final: 0.8426 (mt0) REVERT: A 318 MET cc_start: 0.5684 (tmt) cc_final: 0.5408 (tmt) REVERT: A 440 ASP cc_start: 0.6960 (p0) cc_final: 0.6735 (p0) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.3429 time to fit residues: 20.3290 Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 365 ILE Chi-restraints excluded: chain A residue 406 ILE 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: 1.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150067 restraints weight = 3719.977| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.75 r_work: 0.3507 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3292 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= 0.132 Angle : 0.536 7.409 4383 Z= 0.273 Chirality : 0.039 0.155 563 Planarity : 0.004 0.040 517 Dihedral : 6.674 77.773 587 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.23 % Allowed : 23.17 % 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 are not related in a simple way. whole: 2.15 (0.42), residues: 401 helix: 1.89 (0.28), residues: 330 sheet: -0.99 (1.23), residues: 18 loop : -0.54 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.023 0.001 TYR A 97 PHE 0.011 0.001 PHE A 218 TRP 0.010 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 3219) covalent geometry : angle 0.53585 / 0.27 ( 4383) hydrogen bonds : bond 0.04147 / 2.79 ( 242) hydrogen bonds : angle 3.96223 / 2.84 ( 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 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.134 Fit side-chains REVERT: A 39 ARG cc_start: 0.8066 (ptm-80) cc_final: 0.7746 (ptm160) REVERT: A 161 GLN cc_start: 0.8726 (mt0) cc_final: 0.8474 (mt0) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.3838 time to fit residues: 22.3295 Evaluate side-chains 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.183586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148530 restraints weight = 3660.589| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.76 r_work: 0.3518 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3355 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= 0.136 Angle : 0.546 7.571 4383 Z= 0.277 Chirality : 0.039 0.128 563 Planarity : 0.004 0.040 517 Dihedral : 6.347 70.119 587 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.64 % Allowed : 22.87 % 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 are not related in a simple way. whole: 2.06 (0.42), residues: 401 helix: 1.81 (0.28), residues: 331 sheet: -0.95 (1.24), residues: 18 loop : -0.48 (0.91), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.024 0.002 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.010 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3219) covalent geometry : angle 0.54575 / 0.28 ( 4383) hydrogen bonds : bond 0.04194 / 2.80 ( 242) hydrogen bonds : angle 4.02049 / 2.87 ( 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 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.074 Fit side-chains REVERT: A 39 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7716 (ptm160) REVERT: A 161 GLN cc_start: 0.8722 (mt0) cc_final: 0.8469 (mt0) outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.4131 time to fit residues: 23.1277 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.184980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147427 restraints weight = 3684.603| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.37 r_work: 0.3543 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3219 Z= 0.131 Angle : 0.549 8.666 4383 Z= 0.275 Chirality : 0.039 0.131 563 Planarity : 0.004 0.040 517 Dihedral : 5.573 51.903 587 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.64 % Allowed : 23.17 % 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 are not related in a simple way. whole: 2.08 (0.42), residues: 401 helix: 1.83 (0.28), residues: 331 sheet: -0.90 (1.24), residues: 18 loop : -0.54 (0.90), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.023 0.001 TYR A 97 PHE 0.011 0.001 PHE A 218 TRP 0.013 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 3219) covalent geometry : angle 0.54860 / 0.28 ( 4383) hydrogen bonds : bond 0.04090 / 2.72 ( 242) hydrogen bonds : angle 3.99572 / 2.86 ( 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 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.117 Fit side-chains REVERT: A 39 ARG cc_start: 0.7970 (ptm-80) cc_final: 0.7630 (ptm160) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.3779 time to fit residues: 21.5548 Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148969 restraints weight = 3731.961| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.57 r_work: 0.3472 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3423 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= 0.143 Angle : 0.559 8.532 4383 Z= 0.282 Chirality : 0.039 0.138 563 Planarity : 0.004 0.040 517 Dihedral : 5.605 57.900 587 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.93 % Allowed : 22.87 % 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 are not related in a simple way. whole: 1.94 (0.42), residues: 401 helix: 1.74 (0.28), residues: 330 sheet: -0.99 (1.23), residues: 18 loop : -0.62 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.026 0.002 TYR A 97 PHE 0.012 0.001 PHE A 218 TRP 0.012 0.001 TRP A 441 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 3219) covalent geometry : angle 0.55933 / 0.28 ( 4383) hydrogen bonds : bond 0.04288 / 2.86 ( 242) hydrogen bonds : angle 4.05502 / 2.90 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.81 seconds wall clock time: 24 minutes 11.70 seconds (1451.70 seconds total)