Starting phenix.real_space_refine on Sat May 10 02:57:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsb_60410/05_2025/8zsb_60410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsb_60410/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zsb_60410/05_2025/8zsb_60410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsb_60410/05_2025/8zsb_60410.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsb_60410/05_2025/8zsb_60410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsb_60410/05_2025/8zsb_60410.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.38, per 1000 atoms: 1.12 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: 1.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.40 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: 1.40 Time building geometry restraints manager: 1.37 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 93 or resid 95 through 422 or resid 601)) selection = (chain 'B' and (resid 5 through 93 or resid 95 through 422 or resid 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: 0.510 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP B 273 HIS 0.058 0.004 HIS B 387 PHE 0.019 0.002 PHE A 19 TYR 0.006 0.001 TYR B 396 ARG 0.005 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.14069 ( 341) hydrogen bonds : angle 6.33166 ( 1018) metal coordination : bond 0.09746 ( 4) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.44309 ( 10) covalent geometry : bond 0.01194 ( 4902) covalent geometry : angle 1.17600 ( 6666) *********************** 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 : 0.528 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: 0.1674 time to fit residues: 28.3097 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 : 0.533 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.194627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146541 restraints weight = 9741.345| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 5.71 r_work: 0.3182 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.553 4911 Z= 0.311 Angle : 0.554 6.591 6676 Z= 0.299 Chirality : 0.044 0.141 798 Planarity : 0.004 0.052 832 Dihedral : 5.732 56.737 664 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.71 % Allowed : 7.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.36), residues: 604 helix: 2.31 (0.25), residues: 410 sheet: -0.18 (0.76), residues: 52 loop : -0.66 (0.62), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.011 0.002 HIS A 370 PHE 0.007 0.001 PHE A 42 TYR 0.008 0.001 TYR B 396 ARG 0.006 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 341) hydrogen bonds : angle 4.30791 ( 1018) metal coordination : bond 0.27675 ( 4) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.57909 ( 10) covalent geometry : bond 0.00374 ( 4902) covalent geometry : angle 0.55410 ( 6666) *********************** 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 138 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.467 Fit side-chains REVERT: A 37 MET cc_start: 0.6784 (mmm) cc_final: 0.5920 (mmt) REVERT: A 111 GLN cc_start: 0.8599 (mt0) cc_final: 0.8380 (mm-40) REVERT: A 350 GLN cc_start: 0.8658 (pm20) cc_final: 0.8449 (pm20) REVERT: B 21 PHE cc_start: 0.8145 (t80) cc_final: 0.7939 (t80) REVERT: B 37 MET cc_start: 0.6757 (mmm) cc_final: 0.5777 (mmt) REVERT: B 338 GLU cc_start: 0.8370 (tp30) cc_final: 0.7966 (tt0) REVERT: B 350 GLN cc_start: 0.8616 (pm20) cc_final: 0.8326 (pm20) REVERT: B 368 GLU cc_start: 0.7683 (pt0) cc_final: 0.7242 (pm20) outliers start: 7 outliers final: 4 residues processed: 134 average time/residue: 0.1644 time to fit residues: 27.9723 Evaluate side-chains 116 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 370 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 52 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.197004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132124 restraints weight = 12706.575| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.11 r_work: 0.3281 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2088 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= 0.129 Angle : 0.526 9.280 6676 Z= 0.278 Chirality : 0.042 0.140 798 Planarity : 0.004 0.047 832 Dihedral : 5.106 51.137 658 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.95 % Allowed : 13.31 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.37), residues: 604 helix: 2.47 (0.26), residues: 412 sheet: -0.16 (0.79), residues: 52 loop : -0.54 (0.62), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.010 0.001 HIS B 370 PHE 0.006 0.001 PHE A 134 TYR 0.006 0.001 TYR A 396 ARG 0.005 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 341) hydrogen bonds : angle 4.10250 ( 1018) metal coordination : bond 0.00700 ( 4) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.43483 ( 10) covalent geometry : bond 0.00282 ( 4902) covalent geometry : angle 0.52655 ( 6666) *********************** 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: 3 poor density : 117 time to evaluate : 0.486 Fit side-chains REVERT: A 37 MET cc_start: 0.6606 (mmm) cc_final: 0.5713 (mmt) REVERT: A 58 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 359 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 37 MET cc_start: 0.6641 (mmm) cc_final: 0.5676 (mmt) REVERT: B 359 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7588 (mt-10) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.1502 time to fit residues: 23.3462 Evaluate side-chains 110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.191993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135858 restraints weight = 8165.631| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.62 r_work: 0.3288 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4911 Z= 0.153 Angle : 0.530 5.765 6676 Z= 0.285 Chirality : 0.043 0.140 798 Planarity : 0.004 0.043 832 Dihedral : 4.372 42.504 654 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.52 % Allowed : 13.88 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.36), residues: 604 helix: 2.45 (0.26), residues: 410 sheet: -0.16 (0.79), residues: 52 loop : -0.73 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.007 0.001 HIS A 135 PHE 0.009 0.001 PHE B 21 TYR 0.006 0.001 TYR A 330 ARG 0.004 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 341) hydrogen bonds : angle 4.09504 ( 1018) metal coordination : bond 0.01724 ( 4) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.53353 ( 10) covalent geometry : bond 0.00352 ( 4902) covalent geometry : angle 0.53029 ( 6666) *********************** 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 : 0.551 Fit side-chains REVERT: A 37 MET cc_start: 0.6868 (mmm) cc_final: 0.5946 (mmt) REVERT: A 58 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 359 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 37 MET cc_start: 0.6850 (mmm) cc_final: 0.5915 (mmt) REVERT: B 359 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7567 (mt-10) outliers start: 6 outliers final: 4 residues processed: 118 average time/residue: 0.1579 time to fit residues: 24.0542 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 : 0.534 ------------------------------------------------------------------------------- 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 31 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.192609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129226 restraints weight = 17029.921| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 5.07 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4911 Z= 0.140 Angle : 0.505 6.322 6676 Z= 0.271 Chirality : 0.042 0.133 798 Planarity : 0.004 0.040 832 Dihedral : 3.929 15.743 652 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.95 % Allowed : 15.59 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.36), residues: 604 helix: 2.38 (0.26), residues: 412 sheet: 0.05 (0.80), residues: 50 loop : -0.67 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.010 0.001 PHE A 21 TYR 0.007 0.001 TYR A 330 ARG 0.004 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 341) hydrogen bonds : angle 4.04273 ( 1018) metal coordination : bond 0.01103 ( 4) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.45987 ( 10) covalent geometry : bond 0.00318 ( 4902) covalent geometry : angle 0.50464 ( 6666) *********************** 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 116 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.485 Fit side-chains REVERT: A 37 MET cc_start: 0.6769 (mmm) cc_final: 0.5797 (mmt) REVERT: A 58 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 359 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 368 GLU cc_start: 0.8010 (pt0) cc_final: 0.7422 (pp20) REVERT: B 37 MET cc_start: 0.6721 (mmm) cc_final: 0.5773 (mmt) REVERT: B 58 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7795 (tm-30) outliers start: 3 outliers final: 2 residues processed: 115 average time/residue: 0.1489 time to fit residues: 22.2563 Evaluate side-chains 112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.0040 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.193902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131745 restraints weight = 12795.508| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.03 r_work: 0.3286 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 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 = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4911 Z= 0.128 Angle : 0.483 5.512 6676 Z= 0.261 Chirality : 0.042 0.147 798 Planarity : 0.004 0.039 832 Dihedral : 3.869 14.969 652 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.52 % Allowed : 16.16 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.36), residues: 604 helix: 2.40 (0.26), residues: 412 sheet: 0.13 (0.82), residues: 50 loop : -0.65 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.007 0.001 HIS B 135 PHE 0.010 0.001 PHE A 21 TYR 0.007 0.001 TYR A 396 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 341) hydrogen bonds : angle 4.00377 ( 1018) metal coordination : bond 0.00900 ( 4) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.41136 ( 10) covalent geometry : bond 0.00290 ( 4902) covalent geometry : angle 0.48350 ( 6666) *********************** 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 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6715 (mmm) cc_final: 0.5721 (mmt) REVERT: A 58 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 359 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 368 GLU cc_start: 0.7900 (pt0) cc_final: 0.7514 (pp20) REVERT: B 37 MET cc_start: 0.6704 (mmm) cc_final: 0.5689 (mmt) REVERT: B 58 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8106 (tm-30) outliers start: 6 outliers final: 5 residues processed: 119 average time/residue: 0.1498 time to fit residues: 23.5065 Evaluate side-chains 118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 19 PHE 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 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4708 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.198711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133480 restraints weight = 15038.062| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.42 r_work: 0.3306 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2889 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= 0.117 Angle : 0.474 5.117 6676 Z= 0.255 Chirality : 0.041 0.134 798 Planarity : 0.004 0.038 832 Dihedral : 3.783 13.289 652 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.14 % Allowed : 17.68 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.36), residues: 604 helix: 2.49 (0.26), residues: 412 sheet: 0.25 (0.83), residues: 50 loop : -0.51 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.005 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.005 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 341) hydrogen bonds : angle 3.94928 ( 1018) metal coordination : bond 0.00697 ( 4) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.36345 ( 10) covalent geometry : bond 0.00258 ( 4902) covalent geometry : angle 0.47379 ( 6666) *********************** 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 127 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6764 (mmm) cc_final: 0.5716 (mmt) REVERT: A 58 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 133 LEU cc_start: 0.8703 (tp) cc_final: 0.8501 (tt) REVERT: A 368 GLU cc_start: 0.8006 (pt0) cc_final: 0.7621 (pp20) REVERT: B 37 MET cc_start: 0.6679 (mmm) cc_final: 0.5637 (mmt) REVERT: B 58 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.1462 time to fit residues: 23.9568 Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.194701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132179 restraints weight = 13244.047| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.12 r_work: 0.3290 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2982 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= 0.125 Angle : 0.479 6.306 6676 Z= 0.259 Chirality : 0.042 0.153 798 Planarity : 0.004 0.037 832 Dihedral : 3.802 13.310 652 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.14 % Allowed : 20.15 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.36), residues: 604 helix: 2.50 (0.26), residues: 412 sheet: 0.14 (0.82), residues: 50 loop : -0.42 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.006 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.006 0.001 TYR B 330 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 341) hydrogen bonds : angle 3.96650 ( 1018) metal coordination : bond 0.00566 ( 4) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.35415 ( 10) covalent geometry : bond 0.00284 ( 4902) covalent geometry : angle 0.47912 ( 6666) *********************** 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 120 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.523 Fit side-chains REVERT: A 37 MET cc_start: 0.6788 (mmm) cc_final: 0.5758 (mmt) REVERT: A 58 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 368 GLU cc_start: 0.7959 (pt0) cc_final: 0.7610 (pp20) REVERT: B 37 MET cc_start: 0.6763 (mmm) cc_final: 0.5733 (mmt) REVERT: B 58 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8142 (tm-30) outliers start: 4 outliers final: 3 residues processed: 118 average time/residue: 0.1426 time to fit residues: 22.1755 Evaluate side-chains 118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 19 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.0040 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.197969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133349 restraints weight = 12705.399| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.05 r_work: 0.3284 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4911 Z= 0.130 Angle : 0.492 5.676 6676 Z= 0.269 Chirality : 0.043 0.162 798 Planarity : 0.004 0.036 832 Dihedral : 3.806 14.228 652 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.52 % Allowed : 20.15 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.36), residues: 604 helix: 2.50 (0.26), residues: 412 sheet: 0.14 (0.82), residues: 50 loop : -0.31 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.005 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.006 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 341) hydrogen bonds : angle 3.97916 ( 1018) metal coordination : bond 0.00609 ( 4) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.37158 ( 10) covalent geometry : bond 0.00297 ( 4902) covalent geometry : angle 0.49247 ( 6666) *********************** 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 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6796 (mmm) cc_final: 0.5758 (mmt) REVERT: A 58 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 37 MET cc_start: 0.6769 (mmm) cc_final: 0.5726 (mmt) REVERT: B 58 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.1371 time to fit residues: 21.5627 Evaluate side-chains 118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 19 PHE 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 14 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.191254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130816 restraints weight = 10749.616| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.92 r_work: 0.3239 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4911 Z= 0.169 Angle : 0.531 5.492 6676 Z= 0.290 Chirality : 0.044 0.196 798 Planarity : 0.004 0.036 832 Dihedral : 3.904 14.336 652 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.33 % Allowed : 21.10 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.36), residues: 604 helix: 2.46 (0.26), residues: 408 sheet: 0.09 (0.82), residues: 50 loop : -0.47 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 PHE 0.012 0.001 PHE B 21 TYR 0.007 0.001 TYR A 330 ARG 0.004 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 341) hydrogen bonds : angle 4.05462 ( 1018) metal coordination : bond 0.00766 ( 4) SS BOND : bond 0.00254 ( 5) SS BOND : angle 0.48121 ( 10) covalent geometry : bond 0.00400 ( 4902) covalent geometry : angle 0.53142 ( 6666) ********************** 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 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 58 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 5 outliers final: 5 residues processed: 115 average time/residue: 0.1398 time to fit residues: 21.3306 Evaluate side-chains 116 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 19 PHE 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 44 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.192959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130496 restraints weight = 12812.451| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.07 r_work: 0.3272 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4911 Z= 0.147 Angle : 0.523 8.355 6676 Z= 0.285 Chirality : 0.043 0.179 798 Planarity : 0.004 0.036 832 Dihedral : 3.898 14.218 652 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 20.91 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.36), residues: 604 helix: 2.42 (0.26), residues: 410 sheet: 0.00 (0.79), residues: 50 loop : -0.31 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.009 0.001 HIS A 387 PHE 0.011 0.001 PHE B 21 TYR 0.007 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 341) hydrogen bonds : angle 4.02497 ( 1018) metal coordination : bond 0.03151 ( 4) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.38754 ( 10) covalent geometry : bond 0.00332 ( 4902) covalent geometry : angle 0.52313 ( 6666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.13 seconds wall clock time: 50 minutes 31.51 seconds (3031.51 seconds total)