Starting phenix.real_space_refine on Fri May 9 20:54:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/05_2025/8wjh_37580.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 29 5.16 5 Cl 1 4.86 5 C 2493 2.51 5 N 643 2.21 5 O 658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3823 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 478} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.69 Number of scatterers: 3824 At special positions: 0 Unit cell: (90.95, 77.04, 88.81, 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) Cl 1 17.00 S 29 16.00 O 658 8.00 N 643 7.00 C 2493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 466.3 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 82.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.618A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 3.601A pdb=" N THR A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Proline residue: A 27 - end of helix Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.522A pdb=" N MET A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 222 Processing helix chain 'A' and resid 223 through 253 removed outlier: 4.552A pdb=" N ALA A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 Proline residue: A 265 - end of helix removed outlier: 3.880A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 426 through 456 removed outlier: 3.716A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 484 removed outlier: 3.556A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 4.036A pdb=" N ARG A 87 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 111 " --> pdb=" O ARG A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 289 hydrogen bonds defined for protein. 858 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: 1.01 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1191 1.35 - 1.47: 985 1.47 - 1.60: 1692 1.60 - 1.72: 0 1.72 - 1.85: 45 Bond restraints: 3913 Sorted by residual: bond pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.34e+00 bond pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.88e+00 bond pdb=" CA LEU A 26 " pdb=" C LEU A 26 " ideal model delta sigma weight residual 1.521 1.543 -0.021 1.11e-02 8.12e+03 3.69e+00 bond pdb=" C VAL A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.10e+00 ... (remaining 3908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 5118 2.87 - 5.75: 170 5.75 - 8.62: 29 8.62 - 11.50: 6 11.50 - 14.37: 4 Bond angle restraints: 5327 Sorted by residual: angle pdb=" C CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sigma weight residual 110.42 124.79 -14.37 1.99e+00 2.53e-01 5.22e+01 angle pdb=" C VAL A 135 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N VAL A 460 " pdb=" CA VAL A 460 " pdb=" C VAL A 460 " ideal model delta sigma weight residual 113.43 107.42 6.01 1.09e+00 8.42e-01 3.04e+01 angle pdb=" C ALA A 390 " pdb=" N THR A 391 " pdb=" CA THR A 391 " ideal model delta sigma weight residual 121.14 112.79 8.35 1.75e+00 3.27e-01 2.27e+01 angle pdb=" N THR A 392 " pdb=" CA THR A 392 " pdb=" C THR A 392 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 ... (remaining 5322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2080 17.34 - 34.68: 149 34.68 - 52.02: 49 52.02 - 69.36: 19 69.36 - 86.70: 8 Dihedral angle restraints: 2305 sinusoidal: 864 harmonic: 1441 Sorted by residual: dihedral pdb=" CB CYS A 85 " pdb=" SG CYS A 85 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 11.55 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 113 " pdb=" CB CYS A 113 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" C CYS A 136 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta harmonic sigma weight residual -122.60 -140.65 18.05 0 2.50e+00 1.60e-01 5.21e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 578 0.116 - 0.232: 47 0.232 - 0.349: 1 0.349 - 0.465: 1 0.465 - 0.581: 2 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA CYS A 136 " pdb=" N CYS A 136 " pdb=" C CYS A 136 " pdb=" CB CYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CG LEU A 296 " pdb=" CB LEU A 296 " pdb=" CD1 LEU A 296 " pdb=" CD2 LEU A 296 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 626 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 459 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C PRO A 459 " 0.084 2.00e-02 2.50e+03 pdb=" O PRO A 459 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL A 460 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 390 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ALA A 390 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 390 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 391 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 94 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLN A 94 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 94 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 754 2.78 - 3.31: 3894 3.31 - 3.84: 6500 3.84 - 4.37: 7086 4.37 - 4.90: 12471 Nonbonded interactions: 30705 Sorted by model distance: nonbonded pdb=" OD1 ASP A 366 " pdb=" NH2 ARG A 486 " model vdw 2.256 3.120 nonbonded pdb=" O MET A 218 " pdb=" OG1 THR A 222 " model vdw 2.306 3.040 nonbonded pdb=" O GLN A 424 " pdb=" NE2 GLN A 427 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 212 " pdb=" OG1 THR A 216 " model vdw 2.374 3.040 nonbonded pdb=" NH2 ARG A 89 " pdb=" O ALA A 108 " model vdw 2.383 3.120 ... (remaining 30700 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: 0.250 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 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 : 0.006 0.070 3915 Z= 0.309 Angle : 1.272 14.373 5331 Z= 0.720 Chirality : 0.069 0.581 629 Planarity : 0.009 0.064 662 Dihedral : 15.606 86.704 1367 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.00 % Allowed : 19.75 % Favored : 79.25 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.35), residues: 499 helix: 0.78 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 282 HIS 0.003 0.001 HIS A 47 PHE 0.031 0.003 PHE A 354 TYR 0.021 0.005 TYR A 119 ARG 0.017 0.003 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.13655 ( 289) hydrogen bonds : angle 6.15032 ( 858) SS BOND : bond 0.00528 ( 2) SS BOND : angle 3.56806 ( 4) covalent geometry : bond 0.00615 ( 3913) covalent geometry : angle 1.26836 ( 5327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.394 Fit side-chains REVERT: A 473 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6036 (mtp180) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 0.1452 time to fit residues: 6.4757 Evaluate side-chains 30 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.195668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139469 restraints weight = 3741.972| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.25 r_work: 0.3489 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3915 Z= 0.161 Angle : 0.644 7.056 5331 Z= 0.329 Chirality : 0.041 0.189 629 Planarity : 0.004 0.030 662 Dihedral : 5.345 58.324 538 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.00 % Allowed : 17.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.38), residues: 499 helix: 1.67 (0.27), residues: 375 sheet: -0.34 (1.52), residues: 10 loop : -0.17 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.018 0.002 PHE A 267 TYR 0.011 0.002 TYR A 361 ARG 0.002 0.000 ARG A 48 Details of bonding type rmsd hydrogen bonds : bond 0.05520 ( 289) hydrogen bonds : angle 4.85540 ( 858) SS BOND : bond 0.01277 ( 2) SS BOND : angle 1.59234 ( 4) covalent geometry : bond 0.00353 ( 3913) covalent geometry : angle 0.64298 ( 5327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.408 Fit side-chains REVERT: A 473 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6659 (mtt180) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.1379 time to fit residues: 6.6914 Evaluate side-chains 32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.194494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139380 restraints weight = 3767.790| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.22 r_work: 0.3489 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3915 Z= 0.136 Angle : 0.588 10.726 5331 Z= 0.290 Chirality : 0.038 0.170 629 Planarity : 0.004 0.034 662 Dihedral : 4.913 52.059 538 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 16.75 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.39), residues: 499 helix: 1.46 (0.27), residues: 390 sheet: -0.75 (1.45), residues: 10 loop : 0.13 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 PHE 0.015 0.001 PHE A 205 TYR 0.011 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 289) hydrogen bonds : angle 4.60419 ( 858) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.89213 ( 4) covalent geometry : bond 0.00290 ( 3913) covalent geometry : angle 0.58764 ( 5327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.409 Fit side-chains REVERT: A 1 MET cc_start: 0.4935 (mtp) cc_final: 0.3770 (pmm) REVERT: A 482 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6834 (tp) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.1168 time to fit residues: 6.5652 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.191413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135569 restraints weight = 3770.920| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.23 r_work: 0.3446 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3915 Z= 0.138 Angle : 0.547 6.397 5331 Z= 0.274 Chirality : 0.038 0.158 629 Planarity : 0.004 0.035 662 Dihedral : 3.924 17.731 534 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.00 % Allowed : 17.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 499 helix: 1.42 (0.27), residues: 390 sheet: -1.29 (1.44), residues: 10 loop : 0.23 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 PHE 0.014 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 289) hydrogen bonds : angle 4.53669 ( 858) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.73456 ( 4) covalent geometry : bond 0.00306 ( 3913) covalent geometry : angle 0.54712 ( 5327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4902 (mtp) cc_final: 0.3754 (pmm) REVERT: A 136 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6771 (t) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1193 time to fit residues: 6.1065 Evaluate side-chains 33 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.0170 chunk 5 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.195387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137642 restraints weight = 3786.982| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.37 r_work: 0.3472 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3915 Z= 0.124 Angle : 0.525 6.559 5331 Z= 0.261 Chirality : 0.037 0.154 629 Planarity : 0.004 0.036 662 Dihedral : 3.800 15.828 534 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 19.50 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.39), residues: 499 helix: 1.59 (0.27), residues: 384 sheet: -1.53 (1.44), residues: 10 loop : 0.42 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 PHE 0.013 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 289) hydrogen bonds : angle 4.42410 ( 858) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.64130 ( 4) covalent geometry : bond 0.00266 ( 3913) covalent geometry : angle 0.52447 ( 5327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4825 (mtp) cc_final: 0.3640 (pmm) REVERT: A 120 ASP cc_start: 0.7718 (m-30) cc_final: 0.6620 (p0) REVERT: A 136 CYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6789 (t) REVERT: A 231 MET cc_start: 0.6606 (mmp) cc_final: 0.6348 (mmp) REVERT: A 317 MET cc_start: 0.5086 (pmm) cc_final: 0.4616 (pmm) REVERT: A 482 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6856 (tp) outliers start: 11 outliers final: 7 residues processed: 40 average time/residue: 0.1114 time to fit residues: 6.3041 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130526 restraints weight = 3839.509| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.34 r_work: 0.3227 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3915 Z= 0.177 Angle : 0.585 6.710 5331 Z= 0.293 Chirality : 0.040 0.141 629 Planarity : 0.004 0.036 662 Dihedral : 3.976 18.439 534 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.25 % Allowed : 20.25 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.38), residues: 499 helix: 1.53 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.16 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.001 HIS A 305 PHE 0.016 0.002 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 289) hydrogen bonds : angle 4.57285 ( 858) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.81480 ( 4) covalent geometry : bond 0.00423 ( 3913) covalent geometry : angle 0.58521 ( 5327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4832 (mtp) cc_final: 0.3534 (pmm) REVERT: A 24 PHE cc_start: 0.7366 (m-80) cc_final: 0.6939 (m-80) REVERT: A 120 ASP cc_start: 0.7682 (m-30) cc_final: 0.6496 (p0) REVERT: A 207 MET cc_start: 0.7740 (ttp) cc_final: 0.7329 (ttm) REVERT: A 211 PHE cc_start: 0.6606 (m-10) cc_final: 0.5755 (m-80) REVERT: A 317 MET cc_start: 0.5136 (pmm) cc_final: 0.4724 (pmm) outliers start: 13 outliers final: 8 residues processed: 42 average time/residue: 0.1153 time to fit residues: 6.8513 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.193148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136074 restraints weight = 3755.430| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.34 r_work: 0.3260 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3915 Z= 0.141 Angle : 0.541 6.212 5331 Z= 0.270 Chirality : 0.038 0.143 629 Planarity : 0.004 0.035 662 Dihedral : 3.880 15.619 534 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.00 % Allowed : 22.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.39), residues: 499 helix: 1.58 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.23 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.013 0.001 PHE A 205 TYR 0.007 0.001 TYR A 451 ARG 0.002 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 289) hydrogen bonds : angle 4.46739 ( 858) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.98897 ( 4) covalent geometry : bond 0.00319 ( 3913) covalent geometry : angle 0.54072 ( 5327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4741 (mtp) cc_final: 0.3503 (pmm) REVERT: A 24 PHE cc_start: 0.7323 (m-80) cc_final: 0.7021 (m-80) REVERT: A 120 ASP cc_start: 0.7696 (m-30) cc_final: 0.6504 (p0) REVERT: A 317 MET cc_start: 0.5377 (pmm) cc_final: 0.4815 (ppp) REVERT: A 482 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6713 (tp) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1180 time to fit residues: 6.5046 Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.0370 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.191382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134156 restraints weight = 3713.445| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.34 r_work: 0.3282 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3915 Z= 0.130 Angle : 0.529 6.080 5331 Z= 0.263 Chirality : 0.037 0.135 629 Planarity : 0.004 0.034 662 Dihedral : 3.812 15.419 534 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.00 % Allowed : 22.50 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.39), residues: 499 helix: 1.68 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.28 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 289) hydrogen bonds : angle 4.39844 ( 858) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.27546 ( 4) covalent geometry : bond 0.00283 ( 3913) covalent geometry : angle 0.52758 ( 5327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4759 (mtp) cc_final: 0.3511 (pmm) REVERT: A 120 ASP cc_start: 0.7622 (m-30) cc_final: 0.6347 (p0) REVERT: A 231 MET cc_start: 0.6015 (mmp) cc_final: 0.5753 (mmp) REVERT: A 317 MET cc_start: 0.5246 (pmm) cc_final: 0.4723 (ppp) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1128 time to fit residues: 5.7701 Evaluate side-chains 35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134691 restraints weight = 3708.890| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.35 r_work: 0.3420 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3915 Z= 0.128 Angle : 0.523 6.326 5331 Z= 0.259 Chirality : 0.037 0.128 629 Planarity : 0.004 0.034 662 Dihedral : 3.744 14.846 534 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.50 % Allowed : 22.25 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.39), residues: 499 helix: 1.73 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.30 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 354 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 289) hydrogen bonds : angle 4.35225 ( 858) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.78637 ( 4) covalent geometry : bond 0.00278 ( 3913) covalent geometry : angle 0.52323 ( 5327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.351 Fit side-chains REVERT: A 1 MET cc_start: 0.5035 (mtp) cc_final: 0.3678 (pmm) REVERT: A 28 CYS cc_start: 0.7725 (m) cc_final: 0.7304 (p) REVERT: A 120 ASP cc_start: 0.7683 (m-30) cc_final: 0.6562 (p0) REVERT: A 317 MET cc_start: 0.5295 (pmm) cc_final: 0.4816 (ppp) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.1067 time to fit residues: 5.7707 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.187441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130720 restraints weight = 3767.380| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.30 r_work: 0.3258 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3915 Z= 0.143 Angle : 0.539 6.599 5331 Z= 0.268 Chirality : 0.038 0.129 629 Planarity : 0.004 0.035 662 Dihedral : 3.798 14.729 534 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.00 % Allowed : 22.50 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.39), residues: 499 helix: 1.76 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.20 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 205 TYR 0.007 0.001 TYR A 361 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 289) hydrogen bonds : angle 4.38251 ( 858) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.06748 ( 4) covalent geometry : bond 0.00326 ( 3913) covalent geometry : angle 0.53868 ( 5327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4820 (mtp) cc_final: 0.3536 (pmm) REVERT: A 24 PHE cc_start: 0.7297 (m-80) cc_final: 0.6839 (m-80) REVERT: A 28 CYS cc_start: 0.7583 (m) cc_final: 0.7074 (p) REVERT: A 120 ASP cc_start: 0.7627 (m-30) cc_final: 0.6449 (p0) outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.1131 time to fit residues: 6.3080 Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.191848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136523 restraints weight = 3750.774| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.25 r_work: 0.3237 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3915 Z= 0.153 Angle : 0.555 6.604 5331 Z= 0.275 Chirality : 0.038 0.130 629 Planarity : 0.004 0.035 662 Dihedral : 3.864 14.781 534 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.00 % Allowed : 22.50 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.39), residues: 499 helix: 1.73 (0.27), residues: 366 sheet: None (None), residues: 0 loop : 0.12 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 205 TYR 0.008 0.001 TYR A 451 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 289) hydrogen bonds : angle 4.43278 ( 858) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.00406 ( 4) covalent geometry : bond 0.00355 ( 3913) covalent geometry : angle 0.55454 ( 5327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.65 seconds wall clock time: 41 minutes 9.81 seconds (2469.81 seconds total)