Starting phenix.real_space_refine on Tue Aug 4 18:14:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.map" model { file = "/net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmk_54064/08_2026/9rmk_54064.cif" } resolution = 3.3 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= -0.002 sd= 0.103 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 P 1 5.49 5 S 26 5.16 5 C 3721 2.51 5 N 939 2.21 5 O 992 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5679 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4660 Classifications: {'peptide': 591} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 560} Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 1.39, per 1000 atoms: 0.24 Number of scatterers: 5679 At special positions: 0 Unit cell: (104.16, 65.1, 85.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 992 8.00 N 939 7.00 C 3721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 588 " - pdb=" SG CYS A 603 " distance=2.07 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.09 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: 0.49 Conformation dependent library (CDL) restraints added in 222.8 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 62.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 44 through 64 Processing helix chain 'A' and resid 72 through 93 removed outlier: 3.540A pdb=" N PHE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 4.243A pdb=" N VAL A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 154 removed outlier: 4.360A pdb=" N LEU A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.790A pdb=" N GLN A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.684A pdb=" N ALA A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 removed outlier: 3.991A pdb=" N PHE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 242 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.975A pdb=" N ASN A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 359 through 379 removed outlier: 3.883A pdb=" N GLY A 363 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 Processing helix chain 'A' and resid 409 through 422 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 433 through 466 removed outlier: 3.667A pdb=" N ALA A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.608A pdb=" N GLU A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 4.498A pdb=" N TYR A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 545 through 560 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.621A pdb=" N LEU A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.679A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 46 through 51 removed outlier: 5.218A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 46 through 51 removed outlier: 5.218A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 975 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: 0.92 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1077 1.33 - 1.45: 1597 1.45 - 1.57: 3113 1.57 - 1.69: 2 1.69 - 1.82: 42 Bond restraints: 5831 Sorted by residual: bond pdb=" CG HIS A 123 " pdb=" CD2 HIS A 123 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" CA SER A 348 " pdb=" CB SER A 348 " ideal model delta sigma weight residual 1.531 1.482 0.049 1.65e-02 3.67e+03 8.93e+00 bond pdb=" CA SER A 445 " pdb=" CB SER A 445 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.87e+00 bond pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta sigma weight residual 1.453 1.486 -0.034 1.18e-02 7.18e+03 8.18e+00 bond pdb=" CA ALA F 35 " pdb=" CB ALA F 35 " ideal model delta sigma weight residual 1.534 1.483 0.051 1.78e-02 3.16e+03 8.18e+00 ... (remaining 5826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 7038 1.71 - 3.43: 779 3.43 - 5.14: 96 5.14 - 6.85: 17 6.85 - 8.57: 3 Bond angle restraints: 7933 Sorted by residual: angle pdb=" NE ARG F 107 " pdb=" CZ ARG F 107 " pdb=" NH2 ARG F 107 " ideal model delta sigma weight residual 119.20 112.76 6.44 9.00e-01 1.23e+00 5.11e+01 angle pdb=" NE ARG F 107 " pdb=" CZ ARG F 107 " pdb=" NH1 ARG F 107 " ideal model delta sigma weight residual 121.50 126.31 -4.81 1.00e+00 1.00e+00 2.32e+01 angle pdb=" N ILE A 202 " pdb=" CA ILE A 202 " pdb=" CB ILE A 202 " ideal model delta sigma weight residual 111.83 108.89 2.94 6.90e-01 2.10e+00 1.81e+01 angle pdb=" C HIS A 347 " pdb=" N SER A 348 " pdb=" CA SER A 348 " ideal model delta sigma weight residual 121.56 115.02 6.54 1.56e+00 4.11e-01 1.76e+01 angle pdb=" N VAL F 48 " pdb=" CA VAL F 48 " pdb=" C VAL F 48 " ideal model delta sigma weight residual 111.45 107.69 3.76 9.30e-01 1.16e+00 1.63e+01 ... (remaining 7928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3052 17.55 - 35.10: 302 35.10 - 52.66: 53 52.66 - 70.21: 11 70.21 - 87.76: 7 Dihedral angle restraints: 3425 sinusoidal: 1330 harmonic: 2095 Sorted by residual: dihedral pdb=" CD ARG F 38 " pdb=" NE ARG F 38 " pdb=" CZ ARG F 38 " pdb=" NH1 ARG F 38 " ideal model delta sinusoidal sigma weight residual 0.00 -87.29 87.29 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " pdb=" CZ ARG F 45 " pdb=" NH1 ARG F 45 " ideal model delta sinusoidal sigma weight residual 0.00 84.64 -84.64 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CD ARG F 107 " pdb=" NE ARG F 107 " pdb=" CZ ARG F 107 " pdb=" NH1 ARG F 107 " ideal model delta sinusoidal sigma weight residual 0.00 -55.69 55.69 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 3422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 427 0.044 - 0.088: 286 0.088 - 0.132: 119 0.132 - 0.176: 47 0.176 - 0.220: 13 Chirality restraints: 892 Sorted by residual: chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU A 483 " pdb=" N GLU A 483 " pdb=" C GLU A 483 " pdb=" CB GLU A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" C PRO A 582 " pdb=" CB PRO A 582 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 889 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 107 " 1.050 9.50e-02 1.11e+02 4.72e-01 1.55e+02 pdb=" NE ARG F 107 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG F 107 " -0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG F 107 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG F 107 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 38 " 1.103 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG F 38 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG F 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 38 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG F 38 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 45 " -1.045 9.50e-02 1.11e+02 4.69e-01 1.44e+02 pdb=" NE ARG F 45 " 0.083 2.00e-02 2.50e+03 pdb=" CZ ARG F 45 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG F 45 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 45 " -0.001 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 81 2.66 - 3.22: 5419 3.22 - 3.78: 8912 3.78 - 4.34: 12372 4.34 - 4.90: 20509 Nonbonded interactions: 47293 Sorted by model distance: nonbonded pdb=" O THR A 225 " pdb=" OG1 THR A 228 " model vdw 2.097 3.040 nonbonded pdb=" O HIS A 530 " pdb=" OG1 THR A 533 " model vdw 2.194 3.040 nonbonded pdb=" O THR F 28 " pdb=" ND2 ASN F 77 " model vdw 2.222 3.120 nonbonded pdb=" O ALA A 520 " pdb=" OG SER A 524 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU A 156 " pdb=" N GLY A 169 " model vdw 2.302 3.120 ... (remaining 47288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.410 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.010 0.057 5833 Z= 0.587 Angle : 1.145 8.567 7937 Z= 0.742 Chirality : 0.070 0.220 892 Planarity : 0.029 0.495 986 Dihedral : 14.749 87.759 2073 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.46 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 2.90 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.77 (0.32), residues: 714 helix: 0.36 (0.26), residues: 414 sheet: 0.40 (0.86), residues: 43 loop : -2.10 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.005 ARG F 107 TYR 0.034 0.007 TYR F 102 PHE 0.023 0.007 PHE A 67 TRP 0.035 0.008 TRP A 115 HIS 0.017 0.004 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.59 ( 5831) covalent geometry : angle 1.14462 / 0.74 ( 7933) SS BOND : bond 0.04856 / 2.39 ( 2) SS BOND : angle 1.85660 / 0.96 ( 4) hydrogen bonds : bond 0.14950 / 9.70 ( 330) hydrogen bonds : angle 6.84103 / 5.12 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 553 MET cc_start: 0.8605 (tpt) cc_final: 0.7742 (tpt) REVERT: F 111 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8433 (ttm-80) REVERT: F 114 ASP cc_start: 0.8235 (t70) cc_final: 0.7683 (t0) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0883 time to fit residues: 9.6019 Evaluate side-chains 60 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 199 GLN A 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129015 restraints weight = 8063.555| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.57 r_work: 0.3487 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5833 Z= 0.154 Angle : 0.563 6.235 7937 Z= 0.289 Chirality : 0.040 0.140 892 Planarity : 0.004 0.040 986 Dihedral : 6.508 56.748 815 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.04 % Favored : 94.54 % Rotamer: Outliers : 1.53 % Allowed : 8.35 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.10 (0.32), residues: 714 helix: 1.14 (0.27), residues: 416 sheet: 0.87 (0.84), residues: 43 loop : -1.94 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 38 TYR 0.010 0.001 TYR A 411 PHE 0.010 0.001 PHE A 161 TRP 0.010 0.001 TRP A 552 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 5831) covalent geometry : angle 0.56314 / 0.29 ( 7933) SS BOND : bond 0.00365 / 0.18 ( 2) SS BOND : angle 0.71769 / 0.43 ( 4) hydrogen bonds : bond 0.04294 / 2.75 ( 330) hydrogen bonds : angle 4.33771 / 3.18 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 500 PHE cc_start: 0.8874 (t80) cc_final: 0.8374 (t80) REVERT: A 553 MET cc_start: 0.8694 (tpt) cc_final: 0.7740 (tpt) REVERT: A 587 ASP cc_start: 0.7353 (m-30) cc_final: 0.7102 (m-30) REVERT: F 114 ASP cc_start: 0.8201 (t70) cc_final: 0.7482 (t0) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.0922 time to fit residues: 8.4793 Evaluate side-chains 64 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127558 restraints weight = 8117.482| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.58 r_work: 0.3460 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5833 Z= 0.174 Angle : 0.550 6.075 7937 Z= 0.282 Chirality : 0.040 0.131 892 Planarity : 0.004 0.044 986 Dihedral : 6.549 59.963 815 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.04 % Favored : 94.54 % Rotamer: Outliers : 1.87 % Allowed : 9.88 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.20 (0.32), residues: 714 helix: 1.22 (0.26), residues: 418 sheet: 1.08 (0.81), residues: 43 loop : -1.96 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.011 0.001 TYR A 411 PHE 0.012 0.001 PHE A 496 TRP 0.011 0.001 TRP A 552 HIS 0.002 0.001 HIS A 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 5831) covalent geometry : angle 0.54985 / 0.28 ( 7933) SS BOND : bond 0.00277 / 0.14 ( 2) SS BOND : angle 0.58580 / 0.36 ( 4) hydrogen bonds : bond 0.04162 / 2.66 ( 330) hydrogen bonds : angle 4.06800 / 2.98 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 500 PHE cc_start: 0.8883 (t80) cc_final: 0.8411 (t80) REVERT: A 553 MET cc_start: 0.8631 (tpt) cc_final: 0.8293 (tpt) REVERT: A 587 ASP cc_start: 0.7373 (m-30) cc_final: 0.7100 (m-30) REVERT: F 114 ASP cc_start: 0.8106 (t70) cc_final: 0.7297 (t0) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.0740 time to fit residues: 6.7225 Evaluate side-chains 60 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128172 restraints weight = 8074.101| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.57 r_work: 0.3467 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5833 Z= 0.150 Angle : 0.543 10.108 7937 Z= 0.273 Chirality : 0.039 0.131 892 Planarity : 0.004 0.047 986 Dihedral : 6.392 59.191 815 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.18 % Favored : 94.40 % Rotamer: Outliers : 3.24 % Allowed : 9.37 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.41 (0.32), residues: 714 helix: 1.40 (0.26), residues: 418 sheet: 1.32 (0.82), residues: 43 loop : -1.92 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 111 TYR 0.010 0.001 TYR A 411 PHE 0.011 0.001 PHE A 161 TRP 0.012 0.001 TRP A 552 HIS 0.002 0.001 HIS A 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 5831) covalent geometry : angle 0.54275 / 0.27 ( 7933) SS BOND : bond 0.00268 / 0.13 ( 2) SS BOND : angle 0.59529 / 0.36 ( 4) hydrogen bonds : bond 0.03919 / 2.49 ( 330) hydrogen bonds : angle 3.92517 / 2.87 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.138 Fit side-chains REVERT: A 500 PHE cc_start: 0.8870 (t80) cc_final: 0.8411 (t80) REVERT: A 553 MET cc_start: 0.8634 (tpt) cc_final: 0.7759 (tpt) REVERT: A 587 ASP cc_start: 0.7366 (m-30) cc_final: 0.7081 (m-30) REVERT: F 91 THR cc_start: 0.8763 (p) cc_final: 0.8507 (p) outliers start: 19 outliers final: 15 residues processed: 70 average time/residue: 0.0660 time to fit residues: 6.4029 Evaluate side-chains 68 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.142057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126982 restraints weight = 8253.547| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.59 r_work: 0.3452 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5833 Z= 0.173 Angle : 0.555 8.986 7937 Z= 0.279 Chirality : 0.040 0.134 892 Planarity : 0.004 0.049 986 Dihedral : 6.410 58.965 815 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.46 % Favored : 94.26 % Rotamer: Outliers : 3.24 % Allowed : 10.73 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.32), residues: 714 helix: 1.40 (0.26), residues: 418 sheet: 1.48 (0.83), residues: 43 loop : -1.90 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 45 TYR 0.011 0.001 TYR A 411 PHE 0.012 0.001 PHE A 496 TRP 0.013 0.001 TRP A 552 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 5831) covalent geometry : angle 0.55532 / 0.28 ( 7933) SS BOND : bond 0.00292 / 0.15 ( 2) SS BOND : angle 0.58595 / 0.35 ( 4) hydrogen bonds : bond 0.04032 / 2.56 ( 330) hydrogen bonds : angle 3.90382 / 2.86 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 500 PHE cc_start: 0.8898 (t80) cc_final: 0.8451 (t80) REVERT: A 553 MET cc_start: 0.8626 (tpt) cc_final: 0.7812 (tpt) REVERT: F 91 THR cc_start: 0.8761 (p) cc_final: 0.8514 (p) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.0749 time to fit residues: 7.1309 Evaluate side-chains 69 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 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 = 0.3543 r_free = 0.3543 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116888 restraints weight = 7894.589| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.42 r_work: 0.3294 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5833 Z= 0.127 Angle : 0.520 8.712 7937 Z= 0.261 Chirality : 0.039 0.132 892 Planarity : 0.004 0.049 986 Dihedral : 6.131 59.048 815 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.40 % Rotamer: Outliers : 3.24 % Allowed : 10.90 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.62 (0.32), residues: 714 helix: 1.56 (0.26), residues: 417 sheet: 1.58 (0.84), residues: 43 loop : -1.83 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 111 TYR 0.009 0.001 TYR A 281 PHE 0.009 0.001 PHE A 496 TRP 0.012 0.001 TRP A 552 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 5831) covalent geometry : angle 0.51994 / 0.26 ( 7933) SS BOND : bond 0.00220 / 0.11 ( 2) SS BOND : angle 0.52104 / 0.31 ( 4) hydrogen bonds : bond 0.03668 / 2.32 ( 330) hydrogen bonds : angle 3.78771 / 2.78 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.206 Fit side-chains REVERT: F 91 THR cc_start: 0.8788 (p) cc_final: 0.8501 (p) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.0642 time to fit residues: 6.6190 Evaluate side-chains 65 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 63 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.129112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115326 restraints weight = 7827.881| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.45 r_work: 0.3305 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5833 Z= 0.116 Angle : 0.513 8.186 7937 Z= 0.258 Chirality : 0.038 0.133 892 Planarity : 0.003 0.049 986 Dihedral : 5.878 59.304 815 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.40 % Rotamer: Outliers : 2.90 % Allowed : 11.58 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.75 (0.32), residues: 714 helix: 1.64 (0.26), residues: 417 sheet: 1.63 (0.84), residues: 43 loop : -1.73 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 111 TYR 0.009 0.001 TYR A 281 PHE 0.008 0.001 PHE A 496 TRP 0.012 0.001 TRP A 552 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5831) covalent geometry : angle 0.51281 / 0.26 ( 7933) SS BOND : bond 0.00236 / 0.12 ( 2) SS BOND : angle 0.54037 / 0.32 ( 4) hydrogen bonds : bond 0.03521 / 2.23 ( 330) hydrogen bonds : angle 3.72740 / 2.74 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.214 Fit side-chains REVERT: F 91 THR cc_start: 0.8927 (p) cc_final: 0.8612 (p) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0547 time to fit residues: 5.7887 Evaluate side-chains 71 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 GLN F 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128393 restraints weight = 8118.587| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.57 r_work: 0.3477 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5833 Z= 0.144 Angle : 0.532 7.716 7937 Z= 0.267 Chirality : 0.039 0.133 892 Planarity : 0.004 0.050 986 Dihedral : 5.899 58.639 815 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.60 % Favored : 94.12 % Rotamer: Outliers : 2.90 % Allowed : 12.27 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.67 (0.32), residues: 714 helix: 1.56 (0.26), residues: 417 sheet: 1.67 (0.84), residues: 43 loop : -1.76 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 111 TYR 0.010 0.001 TYR A 411 PHE 0.011 0.001 PHE A 496 TRP 0.014 0.001 TRP A 85 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 5831) covalent geometry : angle 0.53183 / 0.27 ( 7933) SS BOND : bond 0.00335 / 0.17 ( 2) SS BOND : angle 0.70586 / 0.45 ( 4) hydrogen bonds : bond 0.03734 / 2.37 ( 330) hydrogen bonds : angle 3.75702 / 2.76 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.235 Fit side-chains REVERT: A 587 ASP cc_start: 0.7565 (m-30) cc_final: 0.7342 (m-30) REVERT: F 91 THR cc_start: 0.8933 (p) cc_final: 0.8656 (p) outliers start: 17 outliers final: 15 residues processed: 69 average time/residue: 0.0743 time to fit residues: 7.2082 Evaluate side-chains 72 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.144592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129622 restraints weight = 8083.047| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.58 r_work: 0.3495 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5833 Z= 0.119 Angle : 0.513 7.573 7937 Z= 0.257 Chirality : 0.038 0.131 892 Planarity : 0.003 0.049 986 Dihedral : 5.794 58.309 815 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.60 % Favored : 94.12 % Rotamer: Outliers : 2.90 % Allowed : 11.93 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.79 (0.32), residues: 714 helix: 1.67 (0.26), residues: 419 sheet: 1.72 (0.84), residues: 43 loop : -1.76 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 111 TYR 0.009 0.001 TYR A 281 PHE 0.008 0.001 PHE A 59 TRP 0.014 0.001 TRP A 85 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5831) covalent geometry : angle 0.51281 / 0.26 ( 7933) SS BOND : bond 0.00262 / 0.13 ( 2) SS BOND : angle 0.54315 / 0.34 ( 4) hydrogen bonds : bond 0.03519 / 2.23 ( 330) hydrogen bonds : angle 3.69236 / 2.71 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.210 Fit side-chains REVERT: F 91 THR cc_start: 0.8939 (p) cc_final: 0.8663 (p) outliers start: 17 outliers final: 16 residues processed: 71 average time/residue: 0.0727 time to fit residues: 7.2001 Evaluate side-chains 73 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.143671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128606 restraints weight = 8218.303| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.60 r_work: 0.3479 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5833 Z= 0.136 Angle : 0.525 7.441 7937 Z= 0.264 Chirality : 0.039 0.133 892 Planarity : 0.004 0.049 986 Dihedral : 5.833 57.977 815 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.74 % Favored : 93.98 % Rotamer: Outliers : 2.90 % Allowed : 11.93 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.76 (0.32), residues: 714 helix: 1.62 (0.26), residues: 419 sheet: 1.71 (0.83), residues: 43 loop : -1.71 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 111 TYR 0.011 0.001 TYR A 337 PHE 0.011 0.001 PHE A 496 TRP 0.017 0.001 TRP A 85 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5831) covalent geometry : angle 0.52526 / 0.26 ( 7933) SS BOND : bond 0.00286 / 0.14 ( 2) SS BOND : angle 0.53668 / 0.33 ( 4) hydrogen bonds : bond 0.03659 / 2.33 ( 330) hydrogen bonds : angle 3.72309 / 2.73 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.122 Fit side-chains REVERT: A 587 ASP cc_start: 0.7513 (m-30) cc_final: 0.7272 (m-30) REVERT: F 91 THR cc_start: 0.8951 (p) cc_final: 0.8670 (p) outliers start: 17 outliers final: 17 residues processed: 70 average time/residue: 0.0470 time to fit residues: 4.6187 Evaluate side-chains 75 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 0.0040 chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 6 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.0386 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.149633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134340 restraints weight = 7953.703| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.65 r_work: 0.3550 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5833 Z= 0.093 Angle : 0.492 7.367 7937 Z= 0.246 Chirality : 0.037 0.131 892 Planarity : 0.003 0.048 986 Dihedral : 5.376 59.440 815 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % Rotamer: Outliers : 1.53 % Allowed : 13.46 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.12 (0.32), residues: 714 helix: 1.91 (0.26), residues: 420 sheet: 1.79 (0.82), residues: 43 loop : -1.58 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 111 TYR 0.013 0.001 TYR A 337 PHE 0.009 0.001 PHE A 59 TRP 0.015 0.001 TRP A 552 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 5831) covalent geometry : angle 0.49247 / 0.25 ( 7933) SS BOND : bond 0.00195 / 0.10 ( 2) SS BOND : angle 0.41403 / 0.25 ( 4) hydrogen bonds : bond 0.03065 / 1.96 ( 330) hydrogen bonds : angle 3.55036 / 2.60 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.75 seconds wall clock time: 24 minutes 39.66 seconds (1479.66 seconds total)