Starting phenix.real_space_refine on Wed Jul 1 22:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/07_2026/8wjh_37580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/07_2026/8wjh_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_37580/07_2026/8wjh_37580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/07_2026/8wjh_37580.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/07_2026/8wjh_37580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/07_2026/8wjh_37580.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 0.76, per 1000 atoms: 0.20 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: 0.22 Conformation dependent library (CDL) restraints added in 96.2 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: 0.10 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: 0.60 Time building geometry restraints manager: 0.29 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.480 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.017 0.003 ARG A 486 TYR 0.021 0.005 TYR A 119 PHE 0.031 0.003 PHE A 354 TRP 0.032 0.003 TRP A 282 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.31 ( 3913) covalent geometry : angle 1.26836 / 0.72 ( 5327) SS BOND : bond 0.00528 / 0.27 ( 2) SS BOND : angle 3.56806 / 1.74 ( 4) hydrogen bonds : bond 0.13655 / 8.93 ( 289) hydrogen bonds : angle 6.15032 / 4.35 ( 858) *********************** 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 : 0.122 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: 0.0478 time to fit residues: 2.1466 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 : 0.077 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.193695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137341 restraints weight = 3794.567| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.26 r_work: 0.3465 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1507 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= 0.173 Angle : 0.657 6.986 5331 Z= 0.335 Chirality : 0.042 0.183 629 Planarity : 0.004 0.030 662 Dihedral : 5.351 57.533 538 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.00 % Allowed : 17.75 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.38), residues: 499 helix: 1.64 (0.27), residues: 375 sheet: -0.49 (1.49), residues: 10 loop : -0.16 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.012 0.002 TYR A 361 PHE 0.018 0.002 PHE A 267 TRP 0.020 0.002 TRP A 255 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 3913) covalent geometry : angle 0.65531 / 0.33 ( 5327) SS BOND : bond 0.00736 / 0.35 ( 2) SS BOND : angle 1.63146 / 0.72 ( 4) hydrogen bonds : bond 0.05593 / 3.86 ( 289) hydrogen bonds : angle 4.85390 / 3.49 ( 858) *********************** 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 : 0.076 Fit side-chains REVERT: A 473 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6635 (mtt180) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.0448 time to fit residues: 2.1361 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 : 0.088 ------------------------------------------------------------------------------- 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 30 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130077 restraints weight = 3811.290| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.26 r_work: 0.3248 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3915 Z= 0.186 Angle : 0.656 11.666 5331 Z= 0.325 Chirality : 0.041 0.162 629 Planarity : 0.004 0.036 662 Dihedral : 5.092 52.986 538 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.50 % Allowed : 18.25 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.38), residues: 499 helix: 1.27 (0.27), residues: 387 sheet: -1.16 (1.51), residues: 10 loop : 0.05 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.011 0.002 TYR A 361 PHE 0.018 0.002 PHE A 205 TRP 0.013 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 3913) covalent geometry : angle 0.65585 / 0.33 ( 5327) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 1.23130 / 0.56 ( 4) hydrogen bonds : bond 0.05527 / 3.78 ( 289) hydrogen bonds : angle 4.80767 / 3.44 ( 858) *********************** 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 44 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4874 (mtp) cc_final: 0.3762 (pmm) REVERT: A 136 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7071 (t) REVERT: A 411 MET cc_start: 0.6364 (mmp) cc_final: 0.6099 (tpp) REVERT: A 482 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6989 (tp) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.0290 time to fit residues: 1.8386 Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134802 restraints weight = 3841.186| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.30 r_work: 0.3400 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2597 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= 0.141 Angle : 0.558 6.650 5331 Z= 0.279 Chirality : 0.039 0.162 629 Planarity : 0.004 0.034 662 Dihedral : 4.024 17.872 534 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.75 % Allowed : 19.00 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.38), residues: 499 helix: 1.34 (0.27), residues: 390 sheet: -1.34 (1.48), residues: 10 loop : 0.21 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.010 0.001 TYR A 361 PHE 0.013 0.001 PHE A 205 TRP 0.010 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3913) covalent geometry : angle 0.55777 / 0.28 ( 5327) SS BOND : bond 0.00248 / 0.12 ( 2) SS BOND : angle 0.77763 / 0.36 ( 4) hydrogen bonds : bond 0.04789 / 3.28 ( 289) hydrogen bonds : angle 4.61779 / 3.31 ( 858) *********************** 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 42 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4939 (mtp) cc_final: 0.3816 (pmm) REVERT: A 24 PHE cc_start: 0.7612 (m-80) cc_final: 0.7290 (m-80) REVERT: A 136 CYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6859 (t) REVERT: A 411 MET cc_start: 0.6309 (mmp) cc_final: 0.6079 (tpp) outliers start: 11 outliers final: 7 residues processed: 41 average time/residue: 0.0369 time to fit residues: 2.1157 Evaluate side-chains 40 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 500 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136670 restraints weight = 3762.674| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.34 r_work: 0.3269 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2884 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 : 0.562 6.518 5331 Z= 0.278 Chirality : 0.038 0.148 629 Planarity : 0.004 0.035 662 Dihedral : 3.923 17.149 534 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 20.50 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.38), residues: 499 helix: 1.38 (0.27), residues: 390 sheet: -1.67 (1.48), residues: 10 loop : 0.22 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.013 0.001 PHE A 354 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3913) covalent geometry : angle 0.56160 / 0.28 ( 5327) SS BOND : bond 0.00144 / 0.07 ( 2) SS BOND : angle 0.74703 / 0.36 ( 4) hydrogen bonds : bond 0.04744 / 3.25 ( 289) hydrogen bonds : angle 4.54870 / 3.25 ( 858) *********************** 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 39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4693 (mtp) cc_final: 0.3565 (pmm) REVERT: A 136 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7175 (t) REVERT: A 411 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5806 (tpp) REVERT: A 482 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6763 (tp) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 0.0337 time to fit residues: 1.7549 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 : 0.072 ------------------------------------------------------------------------------- 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 411 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131898 restraints weight = 3783.325| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.38 r_work: 0.3233 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3058 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= 0.145 Angle : 0.557 6.896 5331 Z= 0.276 Chirality : 0.038 0.141 629 Planarity : 0.004 0.035 662 Dihedral : 3.920 18.096 534 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.75 % Allowed : 21.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.38), residues: 499 helix: 1.55 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.49 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.008 0.001 TYR A 361 PHE 0.012 0.001 PHE A 205 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 3913) covalent geometry : angle 0.55643 / 0.28 ( 5327) SS BOND : bond 0.00173 / 0.08 ( 2) SS BOND : angle 0.65353 / 0.35 ( 4) hydrogen bonds : bond 0.04754 / 3.26 ( 289) hydrogen bonds : angle 4.50995 / 3.23 ( 858) *********************** 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 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4765 (mtp) cc_final: 0.3575 (pmm) REVERT: A 317 MET cc_start: 0.5083 (pmm) cc_final: 0.4500 (ppp) REVERT: A 411 MET cc_start: 0.6146 (mmp) cc_final: 0.5863 (tpp) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.0284 time to fit residues: 1.5638 Evaluate side-chains 35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 391 THR 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 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 6 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.191410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133516 restraints weight = 3811.586| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.39 r_work: 0.3345 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3173 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 : 0.535 6.384 5331 Z= 0.265 Chirality : 0.037 0.142 629 Planarity : 0.004 0.034 662 Dihedral : 3.853 15.982 534 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.00 % Allowed : 22.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.39), residues: 499 helix: 1.64 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.49 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.012 0.001 PHE A 354 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 3913) covalent geometry : angle 0.53414 / 0.26 ( 5327) SS BOND : bond 0.00151 / 0.07 ( 2) SS BOND : angle 1.16660 / 0.49 ( 4) hydrogen bonds : bond 0.04496 / 3.06 ( 289) hydrogen bonds : angle 4.43714 / 3.19 ( 858) *********************** 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 40 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4891 (mtp) cc_final: 0.3649 (pmm) REVERT: A 120 ASP cc_start: 0.7642 (m-30) cc_final: 0.6388 (p0) REVERT: A 317 MET cc_start: 0.5261 (pmm) cc_final: 0.4654 (ppp) REVERT: A 411 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5815 (tpp) outliers start: 12 outliers final: 6 residues processed: 39 average time/residue: 0.0317 time to fit residues: 1.7897 Evaluate side-chains 32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.195437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137715 restraints weight = 3775.168| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.36 r_work: 0.3273 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.3245 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= 0.129 Angle : 0.527 6.319 5331 Z= 0.261 Chirality : 0.037 0.137 629 Planarity : 0.004 0.035 662 Dihedral : 3.821 15.465 534 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 22.50 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.39), residues: 499 helix: 1.75 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.40 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.012 0.001 PHE A 211 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 3913) covalent geometry : angle 0.52618 / 0.26 ( 5327) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 1.11961 / 0.47 ( 4) hydrogen bonds : bond 0.04436 / 3.01 ( 289) hydrogen bonds : angle 4.39225 / 3.15 ( 858) *********************** 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: 11 poor density : 26 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4736 (mtp) cc_final: 0.3506 (pmm) REVERT: A 107 GLU cc_start: 0.4390 (OUTLIER) cc_final: 0.4188 (tp30) REVERT: A 317 MET cc_start: 0.5350 (pmm) cc_final: 0.4827 (ppp) REVERT: A 411 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5792 (tpp) outliers start: 11 outliers final: 8 residues processed: 36 average time/residue: 0.0301 time to fit residues: 1.6546 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU 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 500 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 chunk 32 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139508 restraints weight = 3776.404| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.38 r_work: 0.3305 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3338 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= 0.120 Angle : 0.516 6.207 5331 Z= 0.255 Chirality : 0.037 0.130 629 Planarity : 0.004 0.035 662 Dihedral : 3.725 14.912 534 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.39), residues: 499 helix: 1.76 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.57 (0.66), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.012 0.001 PHE A 354 TRP 0.009 0.001 TRP A 282 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 3913) covalent geometry : angle 0.51567 / 0.25 ( 5327) SS BOND : bond 0.00155 / 0.07 ( 2) SS BOND : angle 0.77015 / 0.37 ( 4) hydrogen bonds : bond 0.04266 / 2.89 ( 289) hydrogen bonds : angle 4.31029 / 3.10 ( 858) *********************** 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 : 0.081 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4821 (mtp) cc_final: 0.3549 (pmm) REVERT: A 28 CYS cc_start: 0.7617 (m) cc_final: 0.7135 (p) REVERT: A 107 GLU cc_start: 0.4483 (OUTLIER) cc_final: 0.4275 (tp30) REVERT: A 120 ASP cc_start: 0.7707 (m-30) cc_final: 0.6610 (p0) REVERT: A 231 MET cc_start: 0.6125 (mmp) cc_final: 0.5842 (mmp) REVERT: A 317 MET cc_start: 0.5517 (pmm) cc_final: 0.5027 (ppp) REVERT: A 411 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5973 (tpp) outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 0.0333 time to fit residues: 1.8028 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU 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 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.195608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137863 restraints weight = 3787.275| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.38 r_work: 0.3276 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3378 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= 0.130 Angle : 0.528 6.617 5331 Z= 0.261 Chirality : 0.037 0.129 629 Planarity : 0.004 0.036 662 Dihedral : 3.741 14.575 534 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.81 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.39), residues: 499 helix: 1.74 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.51 (0.66), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.013 0.001 PHE A 205 TRP 0.009 0.001 TRP A 282 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3913) covalent geometry : angle 0.52724 / 0.26 ( 5327) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 1.01350 / 0.42 ( 4) hydrogen bonds : bond 0.04425 / 3.01 ( 289) hydrogen bonds : angle 4.30717 / 3.08 ( 858) ********************** 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 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4835 (mtp) cc_final: 0.3544 (pmm) REVERT: A 28 CYS cc_start: 0.7559 (m) cc_final: 0.7064 (p) REVERT: A 107 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: A 120 ASP cc_start: 0.7678 (m-30) cc_final: 0.6597 (p0) REVERT: A 207 MET cc_start: 0.7550 (ttp) cc_final: 0.7179 (ttm) REVERT: A 317 MET cc_start: 0.5534 (pmm) cc_final: 0.5056 (ppp) REVERT: A 411 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5939 (tpp) outliers start: 11 outliers final: 8 residues processed: 35 average time/residue: 0.0319 time to fit residues: 1.6826 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU 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 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.194243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138138 restraints weight = 3790.682| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.26 r_work: 0.3282 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3487 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= 0.137 Angle : 0.536 6.600 5331 Z= 0.265 Chirality : 0.037 0.130 629 Planarity : 0.004 0.036 662 Dihedral : 3.763 14.568 534 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.00 % Allowed : 21.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.39), residues: 499 helix: 1.72 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.16 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 361 PHE 0.012 0.001 PHE A 205 TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3913) covalent geometry : angle 0.53592 / 0.26 ( 5327) SS BOND : bond 0.00207 / 0.10 ( 2) SS BOND : angle 0.85693 / 0.38 ( 4) hydrogen bonds : bond 0.04564 / 3.10 ( 289) hydrogen bonds : angle 4.32033 / 3.08 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.28 seconds wall clock time: 17 minutes 5.22 seconds (1025.22 seconds total)