Starting phenix.real_space_refine on Thu Oct 22 19:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wjy_66034/10_2026/9wjy_66034.map" } resolution = 4.1 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= -0.001 sd= 0.042 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: 3 Type Number sf(0) Gaussians C 2524 2.51 5 N 856 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4238 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1823 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 322} Link IDs: {'PTRANS': 22, 'TRANS': 344} Chain breaks: 3 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1115 Unresolved non-hydrogen angles: 1440 Unresolved non-hydrogen dihedrals: 906 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'ASP:plan': 23, 'GLN:plan1': 25, 'HIS:plan': 15, 'ASN:plan1': 14, 'TYR:plan': 7, 'ARG:plan': 14, 'GLU:plan': 13, 'PHE:plan': 11, 'TRP:plan': 3, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 554 Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 2415 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 419} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 465} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1533 Unresolved non-hydrogen angles: 1973 Unresolved non-hydrogen dihedrals: 1265 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLU:plan': 38, 'HIS:plan': 22, 'PHE:plan': 10, 'GLN:plan1': 19, 'ARG:plan': 31, 'ASN:plan1': 14, 'ASP:plan': 19, 'TYR:plan': 12, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 799 Time building chain proxies: 1.39, per 1000 atoms: 0.33 Number of scatterers: 4238 At special positions: 0 Unit cell: (129.47, 89.88, 96.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 858 8.00 N 856 7.00 C 2524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 239.8 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 688 through 708 removed outlier: 4.420A pdb=" N ASP A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 726 Processing helix chain 'A' and resid 729 through 771 removed outlier: 3.502A pdb=" N LEU A 733 " --> pdb=" O ASN A 729 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP A 750 " --> pdb=" O ASP A 746 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 805 through 824 Processing helix chain 'A' and resid 857 through 876 Processing helix chain 'A' and resid 878 through 899 removed outlier: 4.210A pdb=" N SER A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 921 Proline residue: A 905 - end of helix Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 922 through 941 Processing helix chain 'A' and resid 941 through 951 Processing helix chain 'A' and resid 951 through 970 Proline residue: A 965 - end of helix Processing helix chain 'A' and resid 971 through 977 Processing helix chain 'A' and resid 977 through 998 removed outlier: 3.623A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Proline residue: A 992 - end of helix Processing helix chain 'A' and resid 1000 through 1016 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1038 through 1050 Processing helix chain 'A' and resid 1067 through 1072 Processing helix chain 'A' and resid 1075 through 1089 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 44 through 62 removed outlier: 4.316A pdb=" N LYS B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 94 Proline residue: B 79 - end of helix Processing helix chain 'B' and resid 102 through 134 Processing helix chain 'B' and resid 136 through 159 removed outlier: 3.818A pdb=" N GLN B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'B' and resid 201 through 215 Proline residue: B 212 - end of helix Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 236 removed outlier: 4.414A pdb=" N LYS B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 3.670A pdb=" N GLU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 260 through 278 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 304 through 326 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 355 through 394 Proline residue: B 367 - end of helix removed outlier: 6.795A pdb=" N ILE B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 379 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 442 Proline residue: B 419 - end of helix removed outlier: 4.017A pdb=" N CYS B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 470 Processing helix chain 'B' and resid 471 through 484 removed outlier: 4.270A pdb=" N LYS B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Proline residue: B 481 - end of helix Processing helix chain 'B' and resid 486 through 499 525 hydrogen bonds defined for protein. 1575 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: 0.67 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 858 1.28 - 1.34: 849 1.34 - 1.41: 2 1.41 - 1.48: 854 1.48 - 1.55: 1670 Bond restraints: 4233 Sorted by residual: bond pdb=" C LEU A 731 " pdb=" O LEU A 731 " ideal model delta sigma weight residual 1.244 1.207 0.036 9.80e-03 1.04e+04 1.38e+01 bond pdb=" CA ALA A 922 " pdb=" C ALA A 922 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.18e-02 7.18e+03 1.16e+01 bond pdb=" CA PHE A 771 " pdb=" C PHE A 771 " ideal model delta sigma weight residual 1.524 1.499 0.025 8.10e-03 1.52e+04 9.44e+00 bond pdb=" CA LEU A 906 " pdb=" C LEU A 906 " ideal model delta sigma weight residual 1.523 1.486 0.038 1.30e-02 5.92e+03 8.39e+00 bond pdb=" CA LEU A 993 " pdb=" C LEU A 993 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.30e-02 5.92e+03 8.13e+00 ... (remaining 4228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 5237 2.62 - 5.25: 539 5.25 - 7.87: 91 7.87 - 10.50: 19 10.50 - 13.12: 7 Bond angle restraints: 5893 Sorted by residual: angle pdb=" N ARG B 383 " pdb=" CA ARG B 383 " pdb=" C ARG B 383 " ideal model delta sigma weight residual 111.28 98.59 12.69 1.09e+00 8.42e-01 1.36e+02 angle pdb=" N GLY B 101 " pdb=" CA GLY B 101 " pdb=" C GLY B 101 " ideal model delta sigma weight residual 112.73 125.65 -12.92 1.20e+00 6.94e-01 1.16e+02 angle pdb=" N VAL B 278 " pdb=" CA VAL B 278 " pdb=" C VAL B 278 " ideal model delta sigma weight residual 108.96 120.28 -11.32 1.10e+00 8.26e-01 1.06e+02 angle pdb=" N ARG B 43 " pdb=" CA ARG B 43 " pdb=" C ARG B 43 " ideal model delta sigma weight residual 111.28 100.56 10.72 1.09e+00 8.42e-01 9.68e+01 angle pdb=" N ASP A 942 " pdb=" CA ASP A 942 " pdb=" C ASP A 942 " ideal model delta sigma weight residual 111.28 120.90 -9.62 1.09e+00 8.42e-01 7.79e+01 ... (remaining 5888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 2476 15.18 - 30.36: 0 30.36 - 45.54: 0 45.54 - 60.73: 0 60.73 - 75.91: 1 Dihedral angle restraints: 2477 sinusoidal: 2 harmonic: 2475 Sorted by residual: dihedral pdb=" CA ARG B 238 " pdb=" C ARG B 238 " pdb=" N PRO B 239 " pdb=" CA PRO B 239 " ideal model delta harmonic sigma weight residual 0.00 14.33 -14.33 0 5.00e+00 4.00e-02 8.21e+00 dihedral pdb=" C ARG B 383 " pdb=" N ARG B 383 " pdb=" CA ARG B 383 " pdb=" CB ARG B 383 " ideal model delta harmonic sigma weight residual -122.60 -116.83 -5.77 0 2.50e+00 1.60e-01 5.32e+00 dihedral pdb=" N THR B 508 " pdb=" CA THR B 508 " pdb=" C THR B 508 " pdb=" OXT THR B 508 " ideal model delta sinusoidal sigma weight residual -20.00 -95.91 75.91 2 3.00e+01 1.11e-03 5.02e+00 ... (remaining 2474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 506 0.047 - 0.093: 188 0.093 - 0.140: 98 0.140 - 0.186: 17 0.186 - 0.233: 3 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA ALA A 970 " pdb=" N ALA A 970 " pdb=" C ALA A 970 " pdb=" CB ALA A 970 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO B 303 " pdb=" N PRO B 303 " pdb=" C PRO B 303 " pdb=" CB PRO B 303 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP A 942 " pdb=" N ASP A 942 " pdb=" C ASP A 942 " pdb=" CB ASP A 942 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 809 not shown) Planarity restraints: 853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 749 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.95e+00 pdb=" C TYR A 749 " -0.024 2.00e-02 2.50e+03 pdb=" O TYR A 749 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 750 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 212 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C PRO B 212 " 0.023 2.00e-02 2.50e+03 pdb=" O PRO B 212 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 213 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1081 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C VAL A1081 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL A1081 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A1082 " 0.007 2.00e-02 2.50e+03 ... (remaining 850 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.51: 7 1.51 - 2.36: 34 2.36 - 3.21: 5693 3.21 - 4.05: 10991 4.05 - 4.90: 17428 Warning: very small nonbonded interaction distances. Nonbonded interactions: 34153 Sorted by model distance: nonbonded pdb=" N GLU B 20 " pdb=" O ARG B 66 " model vdw 0.667 3.120 nonbonded pdb=" CB ALA B 478 " pdb=" CA GLN B 497 " model vdw 0.859 3.890 nonbonded pdb=" CA PRO B 481 " pdb=" CA ILE B 493 " model vdw 1.157 3.120 nonbonded pdb=" CB PRO B 481 " pdb=" N ILE B 493 " model vdw 1.235 3.520 nonbonded pdb=" CB PRO B 481 " pdb=" CA ILE B 493 " model vdw 1.262 3.096 ... (remaining 34148 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4743 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 : 0.015 0.561 4236 Z= 1.283 Angle : 1.761 13.121 5893 Z= 1.449 Chirality : 0.061 0.233 812 Planarity : 0.003 0.014 853 Dihedral : 4.308 75.907 853 Min Nonbonded Distance : 0.667 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 7.46 (0.24), residues: 846 helix: 5.79 (0.14), residues: 650 sheet: None (None), residues: 0 loop : 1.46 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.01132 / 0.90 ( 4233) covalent geometry : angle 1.76062 / 1.45 ( 5893) hydrogen bonds : bond 0.28458 / 21.85 ( 525) hydrogen bonds : angle 5.19518 / 4.32 ( 1575) Misc. bond : bond 0.34477 / 16.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0172 time to fit residues: 0.3950 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.140611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.126119 restraints weight = 29249.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.124161 restraints weight = 43582.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.124645 restraints weight = 42625.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.123790 restraints weight = 37543.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.124070 restraints weight = 39346.224| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4236 Z= 0.267 Angle : 0.565 5.789 5893 Z= 0.418 Chirality : 0.036 0.153 812 Planarity : 0.005 0.027 853 Dihedral : 7.138 79.801 853 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.73 (0.27), residues: 846 helix: 1.29 (0.19), residues: 689 sheet: None (None), residues: 0 loop : 0.94 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.27 ( 4233) covalent geometry : angle 0.56512 / 0.42 ( 5893) hydrogen bonds : bond 0.08903 / 6.92 ( 525) hydrogen bonds : angle 6.20518 / 5.03 ( 1575) Misc. bond : bond 0.00721 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0148 time to fit residues: 0.4040 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [73, 69, 50, 39, 30, 72, 11, 19, 77, 51, 46] chunk 73 optimal weight: 0.0370 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 3.1864 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.125873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.112353 restraints weight = 30337.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.111492 restraints weight = 49400.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.110813 restraints weight = 44376.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.109908 restraints weight = 43348.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.110175 restraints weight = 40113.451| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4236 Z= 0.286 Angle : 0.598 5.826 5893 Z= 0.442 Chirality : 0.037 0.153 812 Planarity : 0.005 0.030 853 Dihedral : 7.632 78.910 853 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.31 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.02 (0.28), residues: 846 helix: 0.31 (0.19), residues: 693 sheet: None (None), residues: 0 loop : -0.82 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.28 ( 4233) covalent geometry : angle 0.59771 / 0.44 ( 5893) hydrogen bonds : bond 0.08129 / 6.25 ( 525) hydrogen bonds : angle 6.84299 / 5.53 ( 1575) Misc. bond : bond 0.01105 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0207 time to fit residues: 0.5467 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [69, 18, 83, 64, 49, 10, 77, 30, 58, 81, 53] chunk 69 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 overall best weight: 6.7188 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.114859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.101488 restraints weight = 30284.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.101459 restraints weight = 46088.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.101641 restraints weight = 36847.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101653 restraints weight = 28847.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.101736 restraints weight = 28763.984| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.9650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4236 Z= 0.530 Angle : 0.840 7.969 5893 Z= 0.633 Chirality : 0.041 0.197 812 Planarity : 0.007 0.046 853 Dihedral : 9.072 53.131 853 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.45 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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 (0.27), residues: 846 helix: -1.23 (0.18), residues: 674 sheet: None (None), residues: 0 loop : -1.18 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.53 ( 4233) covalent geometry : angle 0.84039 / 0.63 ( 5893) hydrogen bonds : bond 0.10093 / 7.79 ( 525) hydrogen bonds : angle 8.86597 / 7.17 ( 1575) Misc. bond : bond 0.01357 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0163 time to fit residues: 0.4781 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [56, 41, 45, 76, 31, 2, 81, 17, 27, 9, 44] chunk 56 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 0.0000 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.121741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.109059 restraints weight = 30141.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.108285 restraints weight = 42905.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.108258 restraints weight = 43543.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.108095 restraints weight = 34919.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.108351 restraints weight = 33531.960| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.9486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4236 Z= 0.191 Angle : 0.450 7.149 5893 Z= 0.329 Chirality : 0.034 0.123 812 Planarity : 0.003 0.026 853 Dihedral : 6.857 42.969 853 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.21 (0.28), residues: 846 helix: 0.23 (0.19), residues: 681 sheet: None (None), residues: 0 loop : -1.23 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.19 ( 4233) covalent geometry : angle 0.45003 / 0.33 ( 5893) hydrogen bonds : bond 0.06503 / 5.01 ( 525) hydrogen bonds : angle 6.40331 / 5.20 ( 1575) Misc. bond : bond 0.00590 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.158 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0200 time to fit residues: 0.4891 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [24, 57, 4, 13, 16, 80, 70, 36, 63, 74, 44] chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.121609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.108288 restraints weight = 30127.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.106440 restraints weight = 43341.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.106882 restraints weight = 38536.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.107250 restraints weight = 30804.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.107323 restraints weight = 30269.106| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4236 Z= 0.201 Angle : 0.447 6.122 5893 Z= 0.328 Chirality : 0.035 0.120 812 Planarity : 0.003 0.019 853 Dihedral : 6.211 37.709 853 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.38 (0.29), residues: 846 helix: 0.65 (0.20), residues: 697 sheet: None (None), residues: 0 loop : -1.27 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.20 ( 4233) covalent geometry : angle 0.44676 / 0.33 ( 5893) hydrogen bonds : bond 0.06002 / 4.65 ( 525) hydrogen bonds : angle 6.11225 / 4.96 ( 1575) Misc. bond : bond 0.00660 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0186 time to fit residues: 0.4762 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [45, 19, 78, 83, 11, 46, 73, 72, 42, 17, 66] chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 0.0000 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.119684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.105468 restraints weight = 30799.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.103035 restraints weight = 29877.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.103066 restraints weight = 33455.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.102931 restraints weight = 34915.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.102908 restraints weight = 32416.296| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 1.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4236 Z= 0.234 Angle : 0.481 5.815 5893 Z= 0.359 Chirality : 0.035 0.133 812 Planarity : 0.004 0.020 853 Dihedral : 6.417 32.293 853 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.17 (0.29), residues: 846 helix: 0.50 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.26 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.23 ( 4233) covalent geometry : angle 0.48057 / 0.36 ( 5893) hydrogen bonds : bond 0.06245 / 4.83 ( 525) hydrogen bonds : angle 6.42909 / 5.21 ( 1575) Misc. bond : bond 0.00599 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0204 time to fit residues: 0.5442 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [63, 4, 73, 8, 13, 77, 79, 3, 6, 10, 5] chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 = 0.116659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.104015 restraints weight = 30745.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.102673 restraints weight = 45189.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.102517 restraints weight = 44793.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.102189 restraints weight = 39623.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.102406 restraints weight = 38763.330| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 1.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4236 Z= 0.292 Angle : 0.540 5.653 5893 Z= 0.407 Chirality : 0.036 0.139 812 Planarity : 0.004 0.029 853 Dihedral : 6.678 34.017 853 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.50 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.29), residues: 846 helix: 0.24 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.46 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.29 ( 4233) covalent geometry : angle 0.53979 / 0.41 ( 5893) hydrogen bonds : bond 0.06674 / 5.15 ( 525) hydrogen bonds : angle 6.84709 / 5.55 ( 1575) Misc. bond : bond 0.00925 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0197 time to fit residues: 0.5338 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [46, 39, 18, 6, 47, 63, 72, 23, 1, 25, 67] chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.119951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.106064 restraints weight = 31058.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.105711 restraints weight = 48868.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.105813 restraints weight = 40603.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.105653 restraints weight = 33432.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.106031 restraints weight = 29884.490| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 1.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4236 Z= 0.178 Angle : 0.414 5.255 5893 Z= 0.305 Chirality : 0.035 0.118 812 Planarity : 0.003 0.021 853 Dihedral : 5.898 31.003 853 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.30), residues: 846 helix: 0.97 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.51 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.18 ( 4233) covalent geometry : angle 0.41421 / 0.30 ( 5893) hydrogen bonds : bond 0.05643 / 4.36 ( 525) hydrogen bonds : angle 5.93116 / 4.84 ( 1575) Misc. bond : bond 0.00547 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0209 time to fit residues: 0.5520 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [31, 57, 47, 12, 58, 50, 55, 60, 69, 66, 28] chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 69 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.121749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.108223 restraints weight = 31229.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.107927 restraints weight = 50091.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.108060 restraints weight = 40383.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.108259 restraints weight = 32394.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.108716 restraints weight = 30028.499| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 1.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4236 Z= 0.144 Angle : 0.363 4.484 5893 Z= 0.265 Chirality : 0.034 0.112 812 Planarity : 0.002 0.014 853 Dihedral : 5.210 29.537 853 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.55 (0.30), residues: 846 helix: 1.54 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.41 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.14 ( 4233) covalent geometry : angle 0.36341 / 0.27 ( 5893) hydrogen bonds : bond 0.04915 / 3.81 ( 525) hydrogen bonds : angle 5.38653 / 4.41 ( 1575) Misc. bond : bond 0.00510 / 0.26 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0151 time to fit residues: 0.3608 Evaluate side-chains 8 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [68, 59, 24, 70, 60, 6, 39, 3, 65, 56, 69] chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.122327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.108836 restraints weight = 31099.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.108713 restraints weight = 49342.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.108732 restraints weight = 40323.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.108451 restraints weight = 35416.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.108609 restraints weight = 33203.062| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 1.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4236 Z= 0.134 Angle : 0.350 4.171 5893 Z= 0.254 Chirality : 0.034 0.110 812 Planarity : 0.002 0.013 853 Dihedral : 4.922 28.523 853 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.96 (0.30), residues: 846 helix: 1.82 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.24 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 697 PHE 0.000 0.000 PHE A 748 TRP 0.000 0.000 TRP A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.13 ( 4233) covalent geometry : angle 0.35018 / 0.25 ( 5893) hydrogen bonds : bond 0.04749 / 3.68 ( 525) hydrogen bonds : angle 5.14435 / 4.22 ( 1575) Misc. bond : bond 0.00477 / 0.24 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 909.76 seconds wall clock time: 16 minutes 12.76 seconds (972.76 seconds total)