Starting phenix.real_space_refine on Wed Sep 17 05:06:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsb_60410/09_2025/8zsb_60410.map" } resolution = 3.26 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= -0.003 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 42 5.16 5 C 3114 2.51 5 N 810 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4798 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2431 Chain: "B" Number of atoms: 2398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2431 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.46 Number of scatterers: 4798 At special positions: 0 Unit cell: (61.959, 66.307, 119.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 42 16.00 O 830 8.00 N 810 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 430.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 370 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 387 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 387 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 35 through 61 Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.594A pdb=" N GLU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 239 through 273 removed outlier: 3.645A pdb=" N VAL A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.419A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 315' Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.514A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.821A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.811A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 removed outlier: 4.389A pdb=" N MET A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 35 through 61 Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.595A pdb=" N GLU B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 239 through 273 removed outlier: 3.689A pdb=" N VAL B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.419A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.515A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 3.821A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.811A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 removed outlier: 4.389A pdb=" N MET B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 378 removed outlier: 7.065A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 420 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 390 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 378 removed outlier: 3.890A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 382 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR B 416 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 384 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 1018 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: 0.58 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 767 1.27 - 1.41: 1220 1.41 - 1.54: 2841 1.54 - 1.68: 12 1.68 - 1.81: 62 Bond restraints: 4902 Sorted by residual: bond pdb=" CA LEU B 372 " pdb=" C LEU B 372 " ideal model delta sigma weight residual 1.520 1.417 0.104 1.21e-02 6.83e+03 7.37e+01 bond pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 1.524 1.419 0.105 1.24e-02 6.50e+03 7.15e+01 bond pdb=" CA ASN B 244 " pdb=" C ASN B 244 " ideal model delta sigma weight residual 1.524 1.417 0.107 1.29e-02 6.01e+03 6.87e+01 bond pdb=" C LEU B 243 " pdb=" O LEU B 243 " ideal model delta sigma weight residual 1.237 1.140 0.096 1.17e-02 7.31e+03 6.78e+01 bond pdb=" CA ALA B 95 " pdb=" CB ALA B 95 " ideal model delta sigma weight residual 1.528 1.399 0.130 1.59e-02 3.96e+03 6.65e+01 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 6581 4.74 - 9.47: 73 9.47 - 14.21: 11 14.21 - 18.95: 0 18.95 - 23.68: 1 Bond angle restraints: 6666 Sorted by residual: angle pdb=" N HIS A 65 " pdb=" CA HIS A 65 " pdb=" C HIS A 65 " ideal model delta sigma weight residual 112.24 135.92 -23.68 1.28e+00 6.10e-01 3.42e+02 angle pdb=" O PHE B 94 " pdb=" C PHE B 94 " pdb=" CA BPHE B 94 " ideal model delta sigma weight residual 120.55 130.78 -10.23 1.06e+00 8.90e-01 9.31e+01 angle pdb=" O PHE A 94 " pdb=" C PHE A 94 " pdb=" CA BPHE A 94 " ideal model delta sigma weight residual 120.55 130.49 -9.94 1.06e+00 8.90e-01 8.79e+01 angle pdb=" N GLY B 241 " pdb=" CA GLY B 241 " pdb=" C GLY B 241 " ideal model delta sigma weight residual 112.73 101.66 11.07 1.20e+00 6.94e-01 8.51e+01 angle pdb=" O PHE B 94 " pdb=" C PHE B 94 " pdb=" N ALA B 95 " ideal model delta sigma weight residual 122.12 112.72 9.40 1.06e+00 8.90e-01 7.87e+01 ... (remaining 6661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2508 15.48 - 30.97: 291 30.97 - 46.45: 83 46.45 - 61.94: 19 61.94 - 77.42: 6 Dihedral angle restraints: 2907 sinusoidal: 1127 harmonic: 1780 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual 93.00 170.42 -77.42 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" C HIS A 387 " pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.31e+01 dihedral pdb=" C HIS B 387 " pdb=" N HIS B 387 " pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta harmonic sigma weight residual -122.60 -104.80 -17.80 0 2.50e+00 1.60e-01 5.07e+01 ... (remaining 2904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 764 0.131 - 0.262: 24 0.262 - 0.392: 7 0.392 - 0.523: 1 0.523 - 0.654: 2 Chirality restraints: 798 Sorted by residual: chirality pdb=" CA HIS A 65 " pdb=" N HIS A 65 " pdb=" C HIS A 65 " pdb=" CB HIS A 65 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA HIS B 370 " pdb=" N HIS B 370 " pdb=" C HIS B 370 " pdb=" CB HIS B 370 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA HIS A 370 " pdb=" N HIS A 370 " pdb=" C HIS A 370 " pdb=" CB HIS A 370 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 795 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 387 " -0.062 2.00e-02 2.50e+03 5.64e-02 4.78e+01 pdb=" CG HIS A 387 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS A 387 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 387 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 HIS A 387 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS A 387 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 387 " -0.049 2.00e-02 2.50e+03 5.21e-02 4.07e+01 pdb=" CG HIS B 387 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 387 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS B 387 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 387 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 67 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 68 " -0.018 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3658 3.10 - 3.70: 7314 3.70 - 4.30: 10445 4.30 - 4.90: 17076 Nonbonded interactions: 38519 Sorted by model distance: nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 601 " model vdw 1.897 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 2.000 2.230 nonbonded pdb=" O HIS A 43 " pdb=" OG SER A 46 " model vdw 2.231 3.040 nonbonded pdb=" O HIS B 43 " pdb=" OG SER B 46 " model vdw 2.231 3.040 nonbonded pdb=" O ARG A 239 " pdb=" N GLN A 242 " model vdw 2.392 3.120 ... (remaining 38514 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 93 or resid 95 through 601)) selection = (chain 'B' and (resid 5 through 93 or resid 95 through 601)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.100 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.012 0.148 4911 Z= 0.880 Angle : 1.175 23.685 6676 Z= 0.824 Chirality : 0.072 0.654 798 Planarity : 0.007 0.062 832 Dihedral : 14.721 69.860 1736 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.28 % Allowed : 2.09 % Favored : 95.63 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.35), residues: 604 helix: 1.39 (0.25), residues: 404 sheet: 0.02 (0.81), residues: 38 loop : -0.66 (0.56), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.006 0.001 TYR B 396 PHE 0.019 0.002 PHE A 19 TRP 0.004 0.001 TRP B 273 HIS 0.058 0.004 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.01194 ( 4902) covalent geometry : angle 1.17600 ( 6666) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.44309 ( 10) hydrogen bonds : bond 0.14069 ( 341) hydrogen bonds : angle 6.33166 ( 1018) metal coordination : bond 0.09746 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.203 Fit side-chains REVERT: A 37 MET cc_start: 0.6679 (mmm) cc_final: 0.5897 (mmt) REVERT: A 58 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 352 ASP cc_start: 0.8259 (p0) cc_final: 0.8058 (p0) REVERT: A 355 ASN cc_start: 0.8698 (m-40) cc_final: 0.8495 (m-40) REVERT: A 371 GLU cc_start: 0.8252 (tt0) cc_final: 0.7987 (tt0) REVERT: B 37 MET cc_start: 0.6569 (mmm) cc_final: 0.5797 (mmt) REVERT: B 238 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5257 (m-30) outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 0.0810 time to fit residues: 13.7353 Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 370 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135310 restraints weight = 9533.952| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.47 r_work: 0.3267 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.556 4911 Z= 0.311 Angle : 0.555 6.558 6676 Z= 0.299 Chirality : 0.044 0.141 798 Planarity : 0.004 0.053 832 Dihedral : 5.723 56.542 664 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 7.41 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.36), residues: 604 helix: 2.32 (0.25), residues: 410 sheet: -0.17 (0.76), residues: 52 loop : -0.65 (0.62), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 381 TYR 0.009 0.001 TYR A 396 PHE 0.007 0.001 PHE A 42 TRP 0.009 0.001 TRP A 375 HIS 0.011 0.002 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4902) covalent geometry : angle 0.55469 ( 6666) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.57917 ( 10) hydrogen bonds : bond 0.04998 ( 341) hydrogen bonds : angle 4.29401 ( 1018) metal coordination : bond 0.27818 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.190 Fit side-chains REVERT: A 37 MET cc_start: 0.6815 (mmm) cc_final: 0.5966 (mmt) REVERT: A 59 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7494 (ttp80) REVERT: A 111 GLN cc_start: 0.8595 (mt0) cc_final: 0.8392 (mm-40) REVERT: B 37 MET cc_start: 0.6766 (mmm) cc_final: 0.5804 (mmt) REVERT: B 338 GLU cc_start: 0.8168 (tp30) cc_final: 0.7798 (tt0) REVERT: B 350 GLN cc_start: 0.8541 (pm20) cc_final: 0.8280 (pm20) REVERT: B 368 GLU cc_start: 0.7619 (pt0) cc_final: 0.7268 (pm20) REVERT: B 371 GLU cc_start: 0.7862 (tt0) cc_final: 0.7654 (tt0) outliers start: 8 outliers final: 3 residues processed: 136 average time/residue: 0.0755 time to fit residues: 13.1597 Evaluate side-chains 115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.194750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131268 restraints weight = 15005.931| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.67 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4911 Z= 0.148 Angle : 0.543 9.064 6676 Z= 0.288 Chirality : 0.044 0.142 798 Planarity : 0.004 0.047 832 Dihedral : 4.733 44.135 656 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.14 % Allowed : 12.93 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.36), residues: 604 helix: 2.46 (0.26), residues: 408 sheet: -0.07 (0.80), residues: 52 loop : -0.74 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 381 TYR 0.006 0.001 TYR B 396 PHE 0.036 0.001 PHE B 21 TRP 0.008 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4902) covalent geometry : angle 0.54285 ( 6666) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.51185 ( 10) hydrogen bonds : bond 0.04696 ( 341) hydrogen bonds : angle 4.15577 ( 1018) metal coordination : bond 0.00893 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.185 Fit side-chains REVERT: A 37 MET cc_start: 0.6766 (mmm) cc_final: 0.5914 (mmt) REVERT: A 359 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 37 MET cc_start: 0.6827 (mmm) cc_final: 0.5892 (mmt) REVERT: B 359 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7515 (mt-10) outliers start: 4 outliers final: 2 residues processed: 117 average time/residue: 0.0724 time to fit residues: 11.0587 Evaluate side-chains 111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131282 restraints weight = 15651.864| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.76 r_work: 0.3219 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4911 Z= 0.149 Angle : 0.536 7.392 6676 Z= 0.286 Chirality : 0.043 0.135 798 Planarity : 0.004 0.043 832 Dihedral : 4.379 42.227 654 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.52 % Allowed : 14.07 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.36), residues: 604 helix: 2.47 (0.26), residues: 408 sheet: -0.08 (0.80), residues: 52 loop : -0.76 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.012 0.001 TYR A 330 PHE 0.019 0.001 PHE B 21 TRP 0.008 0.001 TRP B 375 HIS 0.007 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4902) covalent geometry : angle 0.53603 ( 6666) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.50614 ( 10) hydrogen bonds : bond 0.04575 ( 341) hydrogen bonds : angle 4.10629 ( 1018) metal coordination : bond 0.01721 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.183 Fit side-chains REVERT: A 37 MET cc_start: 0.6817 (mmm) cc_final: 0.5868 (mmt) REVERT: A 58 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 359 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 37 MET cc_start: 0.6821 (mmm) cc_final: 0.5846 (mmt) REVERT: B 75 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6593 (mt) REVERT: B 359 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7580 (mt-10) outliers start: 6 outliers final: 3 residues processed: 118 average time/residue: 0.0746 time to fit residues: 11.3765 Evaluate side-chains 114 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.0050 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.197657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131760 restraints weight = 15055.186| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.51 r_work: 0.3271 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4911 Z= 0.122 Angle : 0.502 7.410 6676 Z= 0.267 Chirality : 0.041 0.133 798 Planarity : 0.004 0.039 832 Dihedral : 3.872 14.668 652 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.14 % Allowed : 15.59 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.36), residues: 604 helix: 2.49 (0.26), residues: 412 sheet: 0.07 (0.80), residues: 50 loop : -0.63 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.016 0.001 TYR B 330 PHE 0.014 0.001 PHE B 21 TRP 0.007 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4902) covalent geometry : angle 0.50179 ( 6666) SS BOND : bond 0.00174 ( 5) SS BOND : angle 0.35138 ( 10) hydrogen bonds : bond 0.04110 ( 341) hydrogen bonds : angle 4.00202 ( 1018) metal coordination : bond 0.01078 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.174 Fit side-chains REVERT: A 37 MET cc_start: 0.6614 (mmm) cc_final: 0.5584 (mmt) REVERT: A 58 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 359 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 368 GLU cc_start: 0.7920 (pt0) cc_final: 0.7374 (pp20) REVERT: B 37 MET cc_start: 0.6608 (mmm) cc_final: 0.5616 (mmt) REVERT: B 75 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6390 (mt) REVERT: B 359 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7704 (mt-10) outliers start: 4 outliers final: 2 residues processed: 120 average time/residue: 0.0690 time to fit residues: 10.9255 Evaluate side-chains 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.197104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131441 restraints weight = 13579.679| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.28 r_work: 0.3269 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4911 Z= 0.129 Angle : 0.498 6.773 6676 Z= 0.267 Chirality : 0.042 0.133 798 Planarity : 0.004 0.039 832 Dihedral : 3.824 14.511 652 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.14 % Allowed : 16.92 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.36), residues: 604 helix: 2.46 (0.26), residues: 412 sheet: 0.20 (0.82), residues: 50 loop : -0.65 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.006 0.001 TYR B 330 PHE 0.012 0.001 PHE B 21 TRP 0.008 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4902) covalent geometry : angle 0.49823 ( 6666) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.42614 ( 10) hydrogen bonds : bond 0.04196 ( 341) hydrogen bonds : angle 3.99839 ( 1018) metal coordination : bond 0.00822 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6698 (mmm) cc_final: 0.5672 (mmt) REVERT: A 58 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 368 GLU cc_start: 0.7916 (pt0) cc_final: 0.7518 (pp20) REVERT: A 369 VAL cc_start: 0.8308 (t) cc_final: 0.7931 (m) REVERT: B 37 MET cc_start: 0.6765 (mmm) cc_final: 0.5745 (mmt) outliers start: 4 outliers final: 4 residues processed: 122 average time/residue: 0.0652 time to fit residues: 10.5912 Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.193237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129609 restraints weight = 13615.264| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.23 r_work: 0.3235 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4911 Z= 0.134 Angle : 0.498 6.437 6676 Z= 0.267 Chirality : 0.042 0.134 798 Planarity : 0.004 0.038 832 Dihedral : 3.792 13.522 652 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.33 % Allowed : 18.63 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.36), residues: 604 helix: 2.44 (0.26), residues: 412 sheet: 0.25 (0.84), residues: 50 loop : -0.63 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.006 0.001 TYR B 330 PHE 0.014 0.001 PHE B 21 TRP 0.008 0.001 TRP A 375 HIS 0.006 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4902) covalent geometry : angle 0.49768 ( 6666) SS BOND : bond 0.00209 ( 5) SS BOND : angle 0.44462 ( 10) hydrogen bonds : bond 0.04237 ( 341) hydrogen bonds : angle 4.01333 ( 1018) metal coordination : bond 0.00729 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6805 (mmm) cc_final: 0.5781 (mmt) REVERT: A 58 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 368 GLU cc_start: 0.7940 (pt0) cc_final: 0.7537 (pp20) REVERT: B 37 MET cc_start: 0.6748 (mmm) cc_final: 0.5696 (mmt) outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 0.0645 time to fit residues: 10.2789 Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.193254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134880 restraints weight = 10838.385| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.00 r_work: 0.3248 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4911 Z= 0.133 Angle : 0.495 6.404 6676 Z= 0.267 Chirality : 0.042 0.134 798 Planarity : 0.004 0.037 832 Dihedral : 3.792 13.710 652 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 19.77 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.36), residues: 604 helix: 2.39 (0.26), residues: 412 sheet: 0.19 (0.83), residues: 50 loop : -0.54 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.005 0.001 TYR A 330 PHE 0.011 0.001 PHE B 21 TRP 0.008 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4902) covalent geometry : angle 0.49482 ( 6666) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.38406 ( 10) hydrogen bonds : bond 0.04211 ( 341) hydrogen bonds : angle 4.00966 ( 1018) metal coordination : bond 0.00702 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.176 Fit side-chains REVERT: A 37 MET cc_start: 0.6802 (mmm) cc_final: 0.5773 (mmt) REVERT: A 58 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 368 GLU cc_start: 0.7914 (pt0) cc_final: 0.7553 (pp20) REVERT: B 37 MET cc_start: 0.6764 (mmm) cc_final: 0.5741 (mmt) outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 0.0649 time to fit residues: 10.4679 Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.4980 chunk 52 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** 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 = 0.4182 r_free = 0.4182 target = 0.194368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138221 restraints weight = 8805.773| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.65 r_work: 0.3338 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4911 Z= 0.130 Angle : 0.513 6.364 6676 Z= 0.279 Chirality : 0.043 0.187 798 Planarity : 0.004 0.045 832 Dihedral : 3.779 13.130 652 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 20.53 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.36), residues: 604 helix: 2.39 (0.26), residues: 412 sheet: 0.20 (0.83), residues: 50 loop : -0.36 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.006 0.001 TYR A 330 PHE 0.012 0.001 PHE B 21 TRP 0.008 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4902) covalent geometry : angle 0.51288 ( 6666) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.38426 ( 10) hydrogen bonds : bond 0.04151 ( 341) hydrogen bonds : angle 4.01066 ( 1018) metal coordination : bond 0.00648 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6783 (mmm) cc_final: 0.5761 (mmt) REVERT: A 58 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8221 (tm-30) REVERT: B 352 ASP cc_start: 0.8383 (p0) cc_final: 0.8168 (p0) outliers start: 6 outliers final: 6 residues processed: 121 average time/residue: 0.0645 time to fit residues: 10.4941 Evaluate side-chains 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.195598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138975 restraints weight = 8610.561| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.48 r_work: 0.3357 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4911 Z= 0.120 Angle : 0.517 10.426 6676 Z= 0.276 Chirality : 0.042 0.174 798 Planarity : 0.004 0.041 832 Dihedral : 3.750 12.378 652 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.14 % Allowed : 20.72 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.36), residues: 604 helix: 2.41 (0.26), residues: 412 sheet: 0.17 (0.83), residues: 50 loop : -0.26 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.005 0.001 TYR A 396 PHE 0.009 0.001 PHE A 21 TRP 0.007 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4902) covalent geometry : angle 0.51744 ( 6666) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.30200 ( 10) hydrogen bonds : bond 0.03971 ( 341) hydrogen bonds : angle 3.97864 ( 1018) metal coordination : bond 0.00631 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6686 (mmm) cc_final: 0.5680 (mmt) REVERT: A 58 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8222 (tm-30) outliers start: 4 outliers final: 4 residues processed: 129 average time/residue: 0.0621 time to fit residues: 10.7924 Evaluate side-chains 124 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.194357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147222 restraints weight = 6968.334| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.92 r_work: 0.3352 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4911 Z= 0.131 Angle : 0.518 6.371 6676 Z= 0.279 Chirality : 0.042 0.157 798 Planarity : 0.004 0.051 832 Dihedral : 3.748 12.422 652 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 21.48 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.36), residues: 604 helix: 2.40 (0.26), residues: 412 sheet: 0.21 (0.83), residues: 50 loop : -0.30 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.006 0.001 TYR B 330 PHE 0.010 0.001 PHE B 134 TRP 0.008 0.001 TRP B 375 HIS 0.006 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4902) covalent geometry : angle 0.51783 ( 6666) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.33809 ( 10) hydrogen bonds : bond 0.04078 ( 341) hydrogen bonds : angle 3.97964 ( 1018) metal coordination : bond 0.00679 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.91 seconds wall clock time: 26 minutes 18.67 seconds (1578.67 seconds total)