Starting phenix.real_space_refine on Sat Apr 26 23:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/04_2025/8wjh_37580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/04_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_37580/04_2025/8wjh_37580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/04_2025/8wjh_37580.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/04_2025/8wjh_37580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/04_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-5669/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: 2.75, per 1000 atoms: 0.72 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: 0.86 Conformation dependent library (CDL) restraints added in 428.1 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: 0.40 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: 1.12 Time building geometry restraints manager: 1.05 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: 0.320 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: 0.020 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- 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 : 0.386 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: 0.1435 time to fit residues: 6.4177 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 : 0.384 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.194999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139062 restraints weight = 3746.910| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.23 r_work: 0.3483 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3915 Z= 0.167 Angle : 0.640 6.687 5331 Z= 0.329 Chirality : 0.041 0.181 629 Planarity : 0.004 0.030 662 Dihedral : 5.358 58.055 538 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 1.78 (0.38), residues: 499 helix: 1.67 (0.27), residues: 375 sheet: -0.40 (1.51), residues: 10 loop : -0.17 (0.60), 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 0.003 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 289) hydrogen bonds : angle 4.85025 ( 858) SS BOND : bond 0.00905 ( 2) SS BOND : angle 1.59950 ( 4) covalent geometry : bond 0.00362 ( 3913) covalent geometry : angle 0.63919 ( 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 : 0.398 Fit side-chains REVERT: A 473 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6672 (mtt180) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.1348 time to fit residues: 6.4825 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 : 0.396 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.189606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134234 restraints weight = 3781.759| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.21 r_work: 0.3403 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3915 Z= 0.159 Angle : 0.617 10.784 5331 Z= 0.307 Chirality : 0.040 0.163 629 Planarity : 0.004 0.035 662 Dihedral : 4.977 52.057 538 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.75 % Allowed : 17.75 % Favored : 79.50 % 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: 1.56 (0.38), residues: 499 helix: 1.38 (0.27), residues: 390 sheet: -1.01 (1.45), residues: 10 loop : 0.15 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 282 HIS 0.001 0.000 HIS A 305 PHE 0.016 0.002 PHE A 205 TYR 0.010 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 289) hydrogen bonds : angle 4.68427 ( 858) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.11975 ( 4) covalent geometry : bond 0.00359 ( 3913) covalent geometry : angle 0.61685 ( 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 41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4904 (mtp) cc_final: 0.3748 (pmm) REVERT: A 136 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6993 (t) REVERT: A 411 MET cc_start: 0.6299 (mmp) cc_final: 0.6053 (tpp) REVERT: A 482 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7014 (tp) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.1185 time to fit residues: 6.8340 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 : 0.396 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.189049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132847 restraints weight = 3777.949| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.25 r_work: 0.3389 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3915 Z= 0.143 Angle : 0.553 6.462 5331 Z= 0.279 Chirality : 0.038 0.160 629 Planarity : 0.004 0.037 662 Dihedral : 3.964 17.661 534 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.00 % Allowed : 19.25 % Favored : 78.75 % 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: 1.54 (0.38), residues: 499 helix: 1.36 (0.27), residues: 390 sheet: -1.24 (1.45), residues: 10 loop : 0.21 (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 0.04785 ( 289) hydrogen bonds : angle 4.56848 ( 858) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.76277 ( 4) covalent geometry : bond 0.00323 ( 3913) covalent geometry : angle 0.55293 ( 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 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4820 (mtp) cc_final: 0.3636 (pmm) REVERT: A 136 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7106 (t) REVERT: A 411 MET cc_start: 0.6494 (mmp) cc_final: 0.6192 (tpp) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.1284 time to fit residues: 6.3450 Evaluate side-chains 31 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.194367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136082 restraints weight = 3843.014| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.40 r_work: 0.3242 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3915 Z= 0.141 Angle : 0.554 7.035 5331 Z= 0.276 Chirality : 0.038 0.143 629 Planarity : 0.004 0.037 662 Dihedral : 3.863 16.986 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.25 % Allowed : 21.25 % 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: 1.86 (0.38), residues: 499 helix: 1.54 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.44 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 282 HIS 0.001 0.000 HIS A 305 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 0.04686 ( 289) hydrogen bonds : angle 4.48969 ( 858) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.76796 ( 4) covalent geometry : bond 0.00315 ( 3913) covalent geometry : angle 0.55365 ( 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 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4681 (mtp) cc_final: 0.3524 (pmm) REVERT: A 136 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7156 (t) REVERT: A 231 MET cc_start: 0.6046 (mmp) cc_final: 0.5813 (mmp) REVERT: A 317 MET cc_start: 0.5137 (pmm) cc_final: 0.4653 (ppp) REVERT: A 411 MET cc_start: 0.6095 (mmp) cc_final: 0.5810 (tpp) REVERT: A 482 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6685 (tp) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1132 time to fit residues: 5.9067 Evaluate side-chains 33 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 482 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.187519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129335 restraints weight = 3842.007| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.39 r_work: 0.3205 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3915 Z= 0.169 Angle : 0.577 6.709 5331 Z= 0.288 Chirality : 0.039 0.140 629 Planarity : 0.004 0.037 662 Dihedral : 4.019 19.192 534 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.00 % Allowed : 21.00 % 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: 1.68 (0.38), residues: 499 helix: 1.50 (0.27), residues: 371 sheet: None (None), residues: 0 loop : 0.17 (0.60), residues: 128 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 0.014 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 289) hydrogen bonds : angle 4.54261 ( 858) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.84699 ( 4) covalent geometry : bond 0.00400 ( 3913) covalent geometry : angle 0.57685 ( 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 42 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4790 (mtp) cc_final: 0.3564 (pmm) REVERT: A 24 PHE cc_start: 0.7146 (m-80) cc_final: 0.6816 (m-80) REVERT: A 136 CYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7140 (t) REVERT: A 317 MET cc_start: 0.5340 (pmm) cc_final: 0.4864 (ppp) REVERT: A 411 MET cc_start: 0.6138 (mmt) cc_final: 0.5818 (tpp) outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.1351 time to fit residues: 7.9739 Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 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 391 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.189466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131396 restraints weight = 3750.339| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.38 r_work: 0.3261 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3915 Z= 0.139 Angle : 0.539 6.406 5331 Z= 0.269 Chirality : 0.038 0.137 629 Planarity : 0.004 0.035 662 Dihedral : 3.903 17.440 534 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.00 % Allowed : 20.25 % Favored : 75.75 % 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: 1.94 (0.39), residues: 499 helix: 1.68 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.29 (0.59), 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 52 PHE 0.012 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.001 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 289) hydrogen bonds : angle 4.45969 ( 858) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.62718 ( 4) covalent geometry : bond 0.00312 ( 3913) covalent geometry : angle 0.53906 ( 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 43 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4890 (mtp) cc_final: 0.3578 (pmm) REVERT: A 120 ASP cc_start: 0.7658 (m-30) cc_final: 0.6492 (p0) REVERT: A 231 MET cc_start: 0.6102 (mmp) cc_final: 0.5877 (mmp) REVERT: A 317 MET cc_start: 0.5447 (pmm) cc_final: 0.4873 (ppp) REVERT: A 411 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5828 (tpp) REVERT: A 473 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6549 (mtt180) outliers start: 16 outliers final: 8 residues processed: 42 average time/residue: 0.1410 time to fit residues: 8.0247 Evaluate side-chains 35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 391 THR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126200 restraints weight = 3724.489| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.31 r_work: 0.3239 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3915 Z= 0.146 Angle : 0.549 6.634 5331 Z= 0.273 Chirality : 0.038 0.131 629 Planarity : 0.004 0.035 662 Dihedral : 3.903 15.539 534 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.00 % Allowed : 21.25 % Favored : 75.75 % 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: 1.92 (0.39), residues: 499 helix: 1.69 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.23 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 289) hydrogen bonds : angle 4.43841 ( 858) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.64648 ( 4) covalent geometry : bond 0.00331 ( 3913) covalent geometry : angle 0.54751 ( 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 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4784 (mtp) cc_final: 0.3543 (pmm) REVERT: A 231 MET cc_start: 0.6148 (mmp) cc_final: 0.5912 (mmp) REVERT: A 317 MET cc_start: 0.5514 (pmm) cc_final: 0.4984 (ppp) REVERT: A 411 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5836 (tpp) REVERT: A 473 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6582 (mtt180) outliers start: 12 outliers final: 7 residues processed: 36 average time/residue: 0.1396 time to fit residues: 6.8094 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 153 ILE 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 411 MET Chi-restraints excluded: chain A residue 473 ARG 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: 0.9980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.191110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133353 restraints weight = 3712.006| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.35 r_work: 0.3250 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3412 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= 0.128 Angle : 0.529 6.373 5331 Z= 0.262 Chirality : 0.037 0.131 629 Planarity : 0.004 0.035 662 Dihedral : 3.848 15.281 534 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 21.75 % 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: 2.03 (0.39), residues: 499 helix: 1.72 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.35 (0.63), residues: 124 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 0.013 0.001 PHE A 211 TYR 0.009 0.001 TYR A 361 ARG 0.007 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 289) hydrogen bonds : angle 4.37879 ( 858) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.18578 ( 4) covalent geometry : bond 0.00274 ( 3913) covalent geometry : angle 0.52803 ( 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 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4833 (mtp) cc_final: 0.3535 (pmm) REVERT: A 28 CYS cc_start: 0.7636 (m) cc_final: 0.7092 (p) REVERT: A 207 MET cc_start: 0.7831 (ttp) cc_final: 0.7406 (ttt) REVERT: A 231 MET cc_start: 0.6099 (mmp) cc_final: 0.5889 (mmp) REVERT: A 317 MET cc_start: 0.5476 (pmm) cc_final: 0.4983 (ppp) REVERT: A 411 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5815 (tpp) outliers start: 11 outliers final: 10 residues processed: 36 average time/residue: 0.1131 time to fit residues: 5.8719 Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 153 ILE 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 391 THR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 509 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.189608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131922 restraints weight = 3772.280| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.34 r_work: 0.3240 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3467 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= 0.140 Angle : 0.539 6.528 5331 Z= 0.267 Chirality : 0.038 0.129 629 Planarity : 0.004 0.035 662 Dihedral : 3.848 14.818 534 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.75 % Allowed : 21.75 % 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: 2.00 (0.39), residues: 499 helix: 1.76 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.22 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 211 TYR 0.009 0.001 TYR A 361 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 289) hydrogen bonds : angle 4.37643 ( 858) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.21724 ( 4) covalent geometry : bond 0.00315 ( 3913) covalent geometry : angle 0.53809 ( 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 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4827 (mtp) cc_final: 0.3557 (pmm) REVERT: A 28 CYS cc_start: 0.7631 (m) cc_final: 0.7119 (p) REVERT: A 231 MET cc_start: 0.6208 (mmp) cc_final: 0.5958 (mmp) REVERT: A 317 MET cc_start: 0.5486 (pmm) cc_final: 0.4970 (ppp) REVERT: A 411 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5884 (tpp) outliers start: 11 outliers final: 10 residues processed: 36 average time/residue: 0.1159 time to fit residues: 5.9526 Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 153 ILE 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 391 THR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 509 LEU 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: 8.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.188443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131255 restraints weight = 3744.771| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.32 r_work: 0.3227 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3915 Z= 0.144 Angle : 0.543 6.728 5331 Z= 0.270 Chirality : 0.038 0.130 629 Planarity : 0.004 0.035 662 Dihedral : 3.861 14.880 534 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.75 % Allowed : 22.00 % 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: 1.98 (0.39), residues: 499 helix: 1.74 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.23 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 PHE 0.012 0.001 PHE A 211 TYR 0.009 0.001 TYR A 361 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 289) hydrogen bonds : angle 4.38311 ( 858) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.11026 ( 4) covalent geometry : bond 0.00328 ( 3913) covalent geometry : angle 0.54207 ( 5327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.23 seconds wall clock time: 44 minutes 12.78 seconds (2652.78 seconds total)