Starting phenix.real_space_refine on Tue Aug 4 21:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmh_66091/08_2026/9wmh_66091.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 36 5.49 5 S 16 5.16 5 C 4277 2.51 5 N 1153 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 6809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6036 Classifications: {'peptide': 741} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 707} Chain breaks: 1 Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.25 Number of scatterers: 6809 At special positions: 0 Unit cell: (76.26, 90.2, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 16 16.00 P 36 15.00 O 1324 8.00 N 1153 7.00 C 4277 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=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 383.4 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 33.9% alpha, 23.6% beta 8 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 107 through 126 removed outlier: 4.454A pdb=" N VAL A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.650A pdb=" N PHE A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.021A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.886A pdb=" N ILE A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.626A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 4.165A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.691A pdb=" N PHE A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 546 removed outlier: 3.539A pdb=" N TYR A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 604 through 624 removed outlier: 3.622A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.550A pdb=" N LEU A 339 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 5.423A pdb=" N GLU A 155 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 7.248A pdb=" N PHE A 66 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE A 26 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 68 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR A 21 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU A 95 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 23 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.927A pdb=" N LYS A 224 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 267 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE A 222 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR A 269 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 220 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 429 through 434 removed outlier: 6.422A pdb=" N TYR A 394 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 466 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 396 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 590 removed outlier: 4.330A pdb=" N GLN A 583 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 567 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 630 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 669 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 632 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 671 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 634 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 666 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 732 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 668 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1032 1.31 - 1.44: 2103 1.44 - 1.56: 3809 1.56 - 1.69: 69 1.69 - 1.81: 28 Bond restraints: 7041 Sorted by residual: bond pdb=" C5 DT B 18 " pdb=" C6 DT B 18 " ideal model delta sigma weight residual 1.339 1.386 -0.047 7.00e-03 2.04e+04 4.59e+01 bond pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " ideal model delta sigma weight residual 1.382 1.334 0.048 8.00e-03 1.56e+04 3.53e+01 bond pdb=" N1 DT B 18 " pdb=" C6 DT B 18 " ideal model delta sigma weight residual 1.378 1.340 0.038 7.00e-03 2.04e+04 2.94e+01 bond pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " ideal model delta sigma weight residual 1.373 1.333 0.040 8.00e-03 1.56e+04 2.48e+01 bond pdb=" O3' DT B 1 " pdb=" P DG B 2 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.20e-02 6.94e+03 2.30e+01 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9272 2.12 - 4.24: 370 4.24 - 6.37: 28 6.37 - 8.49: 7 8.49 - 10.61: 1 Bond angle restraints: 9678 Sorted by residual: angle pdb=" N1 DT B 18 " pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " ideal model delta sigma weight residual 114.60 121.62 -7.02 6.00e-01 2.78e+00 1.37e+02 angle pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " ideal model delta sigma weight residual 127.20 120.98 6.22 6.00e-01 2.78e+00 1.08e+02 angle pdb=" O4 DT B 18 " pdb=" C4 DT B 18 " pdb=" C5 DT B 18 " ideal model delta sigma weight residual 124.90 119.93 4.97 7.00e-01 2.04e+00 5.04e+01 angle pdb=" C TYR A 270 " pdb=" CA TYR A 270 " pdb=" CB TYR A 270 " ideal model delta sigma weight residual 109.42 120.03 -10.61 1.57e+00 4.06e-01 4.57e+01 angle pdb=" N1 DT B 18 " pdb=" C6 DT B 18 " pdb=" C5 DT B 18 " ideal model delta sigma weight residual 123.70 119.67 4.03 6.00e-01 2.78e+00 4.50e+01 ... (remaining 9673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 4016 34.77 - 69.54: 143 69.54 - 104.31: 19 104.31 - 139.08: 0 139.08 - 173.85: 5 Dihedral angle restraints: 4183 sinusoidal: 2003 harmonic: 2180 Sorted by residual: dihedral pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sinusoidal sigma weight residual 200.00 26.15 173.85 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U C 12 " pdb=" C1' U C 12 " pdb=" N1 U C 12 " pdb=" C2 U C 12 " ideal model delta sinusoidal sigma weight residual 200.00 26.74 173.26 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C C 15 " pdb=" C1' C C 15 " pdb=" N1 C C 15 " pdb=" C2 C C 15 " ideal model delta sinusoidal sigma weight residual 200.00 36.20 163.80 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 4180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 921 0.073 - 0.146: 126 0.146 - 0.218: 23 0.218 - 0.291: 2 0.291 - 0.364: 3 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL A 495 " pdb=" CA VAL A 495 " pdb=" CG1 VAL A 495 " pdb=" CG2 VAL A 495 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" P DG B 15 " pdb=" OP1 DG B 15 " pdb=" OP2 DG B 15 " pdb=" O5' DG B 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.65 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA TYR A 270 " pdb=" N TYR A 270 " pdb=" C TYR A 270 " pdb=" CB TYR A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1072 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 39 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ASN A 39 " 0.054 2.00e-02 2.50e+03 pdb=" O ASN A 39 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A 40 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 490 " -0.043 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 491 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 45 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ILE A 45 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 45 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 27 2.45 - 3.06: 4340 3.06 - 3.67: 11022 3.67 - 4.29: 17718 4.29 - 4.90: 27416 Nonbonded interactions: 60523 Sorted by model distance: nonbonded pdb=" OD2 ASP A 566 " pdb="CA CA A 801 " model vdw 1.835 2.510 nonbonded pdb=" OP2 DT B 1 " pdb="CA CA B 801 " model vdw 1.985 2.510 nonbonded pdb=" OP1 U C 9 " pdb="CA CA A 801 " model vdw 2.060 2.510 nonbonded pdb=" OP1 DA B 3 " pdb="CA CA B 801 " model vdw 2.061 2.510 nonbonded pdb=" NE2 HIS A 568 " pdb="CA CA A 801 " model vdw 2.152 2.590 ... (remaining 60518 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=0.00 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: 2.530 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.960 Find NCS groups from input model: 0.030 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7041 Z= 0.407 Angle : 0.869 10.610 9678 Z= 0.624 Chirality : 0.057 0.364 1075 Planarity : 0.005 0.066 1104 Dihedral : 18.147 173.854 2779 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 0.60 % Allowed : 1.06 % Favored : 98.34 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 737 helix: 0.31 (0.35), residues: 195 sheet: -0.26 (0.41), residues: 153 loop : -0.52 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.022 0.002 TYR A 113 PHE 0.016 0.002 PHE A 426 TRP 0.012 0.002 TRP A 131 HIS 0.006 0.002 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.41 ( 7041) covalent geometry : angle 0.86924 / 0.62 ( 9678) hydrogen bonds : bond 0.14101 / 8.32 ( 286) hydrogen bonds : angle 7.75279 / 5.43 ( 769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.205 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.5695 time to fit residues: 79.7171 Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 406 ASN A 502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076531 restraints weight = 10940.987| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.84 r_work: 0.2787 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7041 Z= 0.178 Angle : 0.641 7.032 9678 Z= 0.359 Chirality : 0.045 0.154 1075 Planarity : 0.005 0.059 1104 Dihedral : 20.088 177.094 1281 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.87 % Allowed : 11.03 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.04 (0.31), residues: 737 helix: 1.01 (0.35), residues: 198 sheet: -0.42 (0.38), residues: 168 loop : -0.30 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.018 0.002 TYR A 562 PHE 0.024 0.002 PHE A 577 TRP 0.010 0.002 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 7041) covalent geometry : angle 0.64120 / 0.36 ( 9678) hydrogen bonds : bond 0.04722 / 3.15 ( 286) hydrogen bonds : angle 5.90770 / 4.11 ( 769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.245 Fit side-chains REVERT: A 76 MET cc_start: 0.8679 (ppp) cc_final: 0.8298 (ppp) REVERT: A 142 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: A 273 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6760 (mtt-85) REVERT: A 706 GLU cc_start: 0.8378 (tt0) cc_final: 0.8159 (tt0) outliers start: 19 outliers final: 4 residues processed: 84 average time/residue: 0.4740 time to fit residues: 42.4418 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075002 restraints weight = 11239.640| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.78 r_work: 0.2840 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7041 Z= 0.201 Angle : 0.603 8.728 9678 Z= 0.333 Chirality : 0.044 0.146 1075 Planarity : 0.004 0.048 1104 Dihedral : 19.849 175.663 1280 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.27 % Allowed : 12.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.11 (0.30), residues: 737 helix: 1.28 (0.34), residues: 198 sheet: -0.46 (0.38), residues: 168 loop : -0.23 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.013 0.001 TYR A 268 PHE 0.019 0.002 PHE A 577 TRP 0.010 0.002 TRP A 214 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 7041) covalent geometry : angle 0.60288 / 0.33 ( 9678) hydrogen bonds : bond 0.04357 / 2.93 ( 286) hydrogen bonds : angle 5.63105 / 3.90 ( 769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.242 Fit side-chains REVERT: A 76 MET cc_start: 0.8788 (ppp) cc_final: 0.8366 (ppp) REVERT: A 690 GLN cc_start: 0.8310 (pt0) cc_final: 0.7443 (pm20) REVERT: A 706 GLU cc_start: 0.8476 (tt0) cc_final: 0.8252 (tt0) outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 0.5527 time to fit residues: 43.2552 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.105350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075073 restraints weight = 11248.927| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.81 r_work: 0.2851 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7041 Z= 0.177 Angle : 0.578 10.164 9678 Z= 0.321 Chirality : 0.043 0.154 1075 Planarity : 0.004 0.068 1104 Dihedral : 19.689 175.045 1276 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 13.90 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 737 helix: 1.40 (0.34), residues: 198 sheet: -0.39 (0.38), residues: 163 loop : -0.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 522 TYR 0.010 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.008 0.002 TRP A 131 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 7041) covalent geometry : angle 0.57832 / 0.32 ( 9678) hydrogen bonds : bond 0.04118 / 2.78 ( 286) hydrogen bonds : angle 5.53713 / 3.83 ( 769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8814 (ppp) cc_final: 0.8379 (ppp) REVERT: A 95 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 142 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: A 706 GLU cc_start: 0.8451 (tt0) cc_final: 0.8198 (tt0) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.5667 time to fit residues: 37.7802 Evaluate side-chains 59 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075504 restraints weight = 11386.280| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.80 r_work: 0.2854 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7041 Z= 0.168 Angle : 0.552 6.501 9678 Z= 0.310 Chirality : 0.042 0.144 1075 Planarity : 0.004 0.053 1104 Dihedral : 19.590 174.461 1276 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.11 % Allowed : 13.75 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.32 (0.30), residues: 737 helix: 1.55 (0.35), residues: 198 sheet: -0.42 (0.36), residues: 180 loop : -0.11 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 522 TYR 0.009 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.009 0.002 TRP A 214 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 7041) covalent geometry : angle 0.55247 / 0.31 ( 9678) hydrogen bonds : bond 0.04038 / 2.75 ( 286) hydrogen bonds : angle 5.42423 / 3.74 ( 769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8839 (ppp) cc_final: 0.8509 (ppp) REVERT: A 79 ARG cc_start: 0.6836 (mmm160) cc_final: 0.6486 (mtm180) REVERT: A 142 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: A 144 MET cc_start: 0.9105 (mtp) cc_final: 0.8831 (mtt) REVERT: A 690 GLN cc_start: 0.8179 (pt0) cc_final: 0.7387 (pm20) REVERT: A 706 GLU cc_start: 0.8455 (tt0) cc_final: 0.8190 (tt0) outliers start: 14 outliers final: 7 residues processed: 64 average time/residue: 0.4980 time to fit residues: 33.7172 Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 377 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074063 restraints weight = 11379.875| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.83 r_work: 0.2799 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7041 Z= 0.195 Angle : 0.569 9.429 9678 Z= 0.314 Chirality : 0.042 0.141 1075 Planarity : 0.004 0.052 1104 Dihedral : 19.532 174.270 1276 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 13.90 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.37 (0.30), residues: 737 helix: 1.69 (0.35), residues: 198 sheet: -0.42 (0.36), residues: 180 loop : -0.11 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 522 TYR 0.010 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 7041) covalent geometry : angle 0.56938 / 0.31 ( 9678) hydrogen bonds : bond 0.04059 / 2.75 ( 286) hydrogen bonds : angle 5.36360 / 3.68 ( 769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 144 MET cc_start: 0.9064 (mtp) cc_final: 0.8770 (mtt) REVERT: A 207 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 287 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7332 (tpt) REVERT: A 706 GLU cc_start: 0.8487 (tt0) cc_final: 0.8226 (tt0) outliers start: 17 outliers final: 7 residues processed: 63 average time/residue: 0.4864 time to fit residues: 32.4717 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075111 restraints weight = 11270.439| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.76 r_work: 0.2853 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7041 Z= 0.158 Angle : 0.543 7.501 9678 Z= 0.303 Chirality : 0.041 0.142 1075 Planarity : 0.004 0.052 1104 Dihedral : 19.475 174.342 1276 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 14.35 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.42 (0.31), residues: 737 helix: 1.74 (0.35), residues: 198 sheet: -0.39 (0.36), residues: 178 loop : -0.09 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.010 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.011 0.002 TRP A 214 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7041) covalent geometry : angle 0.54310 / 0.30 ( 9678) hydrogen bonds : bond 0.03934 / 2.67 ( 286) hydrogen bonds : angle 5.31232 / 3.65 ( 769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8859 (ppp) cc_final: 0.8510 (ppp) REVERT: A 79 ARG cc_start: 0.6641 (mmm160) cc_final: 0.6368 (mtp85) REVERT: A 95 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: A 144 MET cc_start: 0.9042 (mtp) cc_final: 0.8760 (mtt) REVERT: A 207 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 706 GLU cc_start: 0.8478 (tt0) cc_final: 0.8196 (tt0) outliers start: 15 outliers final: 6 residues processed: 67 average time/residue: 0.4692 time to fit residues: 33.5811 Evaluate side-chains 61 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075270 restraints weight = 11301.389| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.78 r_work: 0.2858 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7041 Z= 0.155 Angle : 0.556 9.501 9678 Z= 0.308 Chirality : 0.041 0.142 1075 Planarity : 0.004 0.059 1104 Dihedral : 19.429 174.691 1276 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 14.65 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.38 (0.30), residues: 737 helix: 1.68 (0.35), residues: 198 sheet: -0.42 (0.36), residues: 178 loop : -0.09 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.018 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.008 0.001 TRP A 131 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7041) covalent geometry : angle 0.55633 / 0.31 ( 9678) hydrogen bonds : bond 0.03889 / 2.64 ( 286) hydrogen bonds : angle 5.28137 / 3.63 ( 769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.162 Fit side-chains REVERT: A 36 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: A 95 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: A 144 MET cc_start: 0.9041 (mtp) cc_final: 0.8758 (mtt) REVERT: A 207 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8885 (mp) REVERT: A 690 GLN cc_start: 0.8163 (pt0) cc_final: 0.7394 (pm20) REVERT: A 706 GLU cc_start: 0.8531 (tt0) cc_final: 0.8282 (tt0) outliers start: 17 outliers final: 7 residues processed: 65 average time/residue: 0.4668 time to fit residues: 32.3039 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.073883 restraints weight = 11310.075| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.80 r_work: 0.2818 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7041 Z= 0.185 Angle : 0.566 8.219 9678 Z= 0.311 Chirality : 0.041 0.139 1075 Planarity : 0.004 0.060 1104 Dihedral : 19.424 174.892 1276 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.11 % Allowed : 14.80 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.40 (0.30), residues: 737 helix: 1.77 (0.35), residues: 198 sheet: -0.43 (0.36), residues: 178 loop : -0.11 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 522 TYR 0.017 0.001 TYR A 113 PHE 0.020 0.001 PHE A 426 TRP 0.008 0.001 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 7041) covalent geometry : angle 0.56578 / 0.31 ( 9678) hydrogen bonds : bond 0.03934 / 2.67 ( 286) hydrogen bonds : angle 5.28147 / 3.63 ( 769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: A 95 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: A 144 MET cc_start: 0.9005 (mtp) cc_final: 0.8746 (mtt) REVERT: A 207 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (mp) REVERT: A 522 ARG cc_start: 0.7252 (mtm110) cc_final: 0.7025 (mtm110) REVERT: A 706 GLU cc_start: 0.8613 (tt0) cc_final: 0.8270 (tt0) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.4831 time to fit residues: 31.2384 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.075529 restraints weight = 11313.301| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.80 r_work: 0.2861 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7041 Z= 0.136 Angle : 0.548 7.871 9678 Z= 0.304 Chirality : 0.041 0.142 1075 Planarity : 0.004 0.055 1104 Dihedral : 19.382 174.985 1276 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 1.66 % Allowed : 15.41 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.42 (0.31), residues: 737 helix: 1.80 (0.35), residues: 197 sheet: -0.46 (0.37), residues: 173 loop : -0.09 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.016 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.014 0.002 TRP A 214 HIS 0.002 0.000 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7041) covalent geometry : angle 0.54844 / 0.30 ( 9678) hydrogen bonds : bond 0.03814 / 2.59 ( 286) hydrogen bonds : angle 5.24958 / 3.60 ( 769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: A 95 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 144 MET cc_start: 0.8992 (mtp) cc_final: 0.8717 (mtt) REVERT: A 207 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 690 GLN cc_start: 0.8150 (pt0) cc_final: 0.7398 (pm20) REVERT: A 706 GLU cc_start: 0.8566 (tt0) cc_final: 0.8244 (tt0) outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 0.4962 time to fit residues: 31.9419 Evaluate side-chains 65 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 729 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.074674 restraints weight = 11346.154| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.77 r_work: 0.2843 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7041 Z= 0.177 Angle : 0.567 8.239 9678 Z= 0.310 Chirality : 0.041 0.139 1075 Planarity : 0.004 0.053 1104 Dihedral : 19.378 175.093 1276 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 1.96 % Allowed : 15.71 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.46 (0.31), residues: 737 helix: 1.82 (0.35), residues: 198 sheet: -0.39 (0.37), residues: 178 loop : -0.08 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.016 0.001 TYR A 113 PHE 0.019 0.001 PHE A 426 TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 7041) covalent geometry : angle 0.56714 / 0.31 ( 9678) hydrogen bonds : bond 0.03873 / 2.63 ( 286) hydrogen bonds : angle 5.24147 / 3.60 ( 769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.44 seconds wall clock time: 37 minutes 46.59 seconds (2266.59 seconds total)