Starting phenix.real_space_refine on Thu Jul 24 12:46:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl0_45657/07_2025/9cl0_45657.cif" } resolution = 2.3 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= 0.002 sd= 0.084 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4218 2.51 5 N 1000 2.21 5 O 1018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6266 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3133 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 6.17, per 1000 atoms: 0.98 Number of scatterers: 6266 At special positions: 0 Unit cell: (125.632, 74.048, 73.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1018 8.00 N 1000 7.00 C 4218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 853.4 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 80.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.244A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 4.255A pdb=" N HIS A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.187A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.692A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.103A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.619A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 581 removed outlier: 4.327A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 Proline residue: A 598 - end of helix removed outlier: 3.806A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 257 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.244A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 4.255A pdb=" N HIS B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.187A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.692A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.103A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.619A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 removed outlier: 4.327A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 619 Proline residue: B 598 - end of helix removed outlier: 3.806A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1353 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: 1.83 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 898 1.31 - 1.44: 2094 1.44 - 1.56: 3436 1.56 - 1.69: 4 1.69 - 1.81: 42 Bond restraints: 6474 Sorted by residual: bond pdb=" CA PHE B 394 " pdb=" C PHE B 394 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.44e-02 4.82e+03 4.07e+01 bond pdb=" CA PHE A 394 " pdb=" C PHE A 394 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.44e-02 4.82e+03 4.07e+01 bond pdb=" C ASP A 393 " pdb=" N PHE A 394 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" C ASP B 393 " pdb=" N PHE B 394 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" C PHE B 394 " pdb=" O PHE B 394 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.18e-02 7.18e+03 1.65e+01 ... (remaining 6469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 8778 7.57 - 15.14: 18 15.14 - 22.71: 4 22.71 - 30.28: 6 30.28 - 37.85: 4 Bond angle restraints: 8810 Sorted by residual: angle pdb=" N PHE A 386 " pdb=" CA PHE A 386 " pdb=" C PHE A 386 " ideal model delta sigma weight residual 112.72 146.86 -34.14 1.14e+00 7.69e-01 8.97e+02 angle pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" C PHE B 386 " ideal model delta sigma weight residual 112.72 146.86 -34.14 1.14e+00 7.69e-01 8.97e+02 angle pdb=" N LEU A 421 " pdb=" CA LEU A 421 " pdb=" C LEU A 421 " ideal model delta sigma weight residual 112.24 150.09 -37.85 1.28e+00 6.10e-01 8.75e+02 angle pdb=" N LEU B 421 " pdb=" CA LEU B 421 " pdb=" C LEU B 421 " ideal model delta sigma weight residual 112.24 150.09 -37.85 1.28e+00 6.10e-01 8.75e+02 angle pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 109.85 80.56 29.29 1.58e+00 4.01e-01 3.44e+02 ... (remaining 8805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 3090 16.28 - 32.56: 426 32.56 - 48.83: 108 48.83 - 65.11: 18 65.11 - 81.39: 8 Dihedral angle restraints: 3650 sinusoidal: 1434 harmonic: 2216 Sorted by residual: dihedral pdb=" N HIS A 387 " pdb=" C HIS A 387 " pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta harmonic sigma weight residual 122.80 83.83 38.97 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N HIS B 387 " pdb=" C HIS B 387 " pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta harmonic sigma weight residual 122.80 83.83 38.97 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N LYS A 422 " pdb=" C LYS A 422 " pdb=" CA LYS A 422 " pdb=" CB LYS A 422 " ideal model delta harmonic sigma weight residual 122.80 153.78 -30.98 0 2.50e+00 1.60e-01 1.54e+02 ... (remaining 3647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 956 0.262 - 0.525: 6 0.525 - 0.787: 0 0.787 - 1.049: 2 1.049 - 1.311: 4 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA LYS A 422 " pdb=" N LYS A 422 " pdb=" C LYS A 422 " pdb=" CB LYS A 422 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" CA LYS B 422 " pdb=" N LYS B 422 " pdb=" C LYS B 422 " pdb=" CB LYS B 422 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" CA LEU A 421 " pdb=" N LEU A 421 " pdb=" C LEU A 421 " pdb=" CB LEU A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 ... (remaining 965 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 263 " -0.625 9.50e-02 1.11e+02 2.80e-01 4.80e+01 pdb=" NE ARG B 263 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 263 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 263 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 263 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 263 " 0.625 9.50e-02 1.11e+02 2.80e-01 4.80e+01 pdb=" NE ARG A 263 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 263 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 263 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 263 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 468 " 0.611 9.50e-02 1.11e+02 2.74e-01 4.61e+01 pdb=" NE ARG B 468 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 468 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 468 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 468 " 0.023 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 48 2.59 - 3.17: 5328 3.17 - 3.75: 10464 3.75 - 4.32: 13991 4.32 - 4.90: 22470 Nonbonded interactions: 52301 Sorted by model distance: nonbonded pdb=" N HIS A 387 " pdb=" O HIS A 387 " model vdw 2.015 2.496 nonbonded pdb=" N HIS B 387 " pdb=" O HIS B 387 " model vdw 2.015 2.496 nonbonded pdb=" O THR A 261 " pdb=" OD1 ASP A 262 " model vdw 2.087 3.040 nonbonded pdb=" O THR B 261 " pdb=" OD1 ASP B 262 " model vdw 2.087 3.040 nonbonded pdb=" CD LYS B 258 " pdb=" CE1 PHE B 336 " model vdw 2.097 2.992 ... (remaining 52296 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 177.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:21.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.008 0.352 6476 Z= 0.700 Angle : 1.456 37.854 8810 Z= 1.001 Chirality : 0.100 1.311 968 Planarity : 0.019 0.280 1070 Dihedral : 16.084 81.389 2222 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 2.41 % Allowed : 18.67 % Favored : 78.92 % Cbeta Deviations : 1.40 % Peptide Plane: Cis-proline : 8.33 % 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: 1.78 (0.31), residues: 742 helix: 2.11 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.29 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 607 HIS 0.002 0.001 HIS B 313 PHE 0.039 0.002 PHE B 394 TYR 0.020 0.002 TYR A 368 ARG 0.009 0.001 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.10970 ( 451) hydrogen bonds : angle 5.20112 ( 1353) covalent geometry : bond 0.00498 ( 6474) covalent geometry : angle 1.45569 ( 8810) Misc. bond : bond 0.35193 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.706 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 1.2155 time to fit residues: 102.5312 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.198076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.187843 restraints weight = 4877.261| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 0.42 r_work: 0.3807 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6476 Z= 0.159 Angle : 0.585 6.878 8810 Z= 0.318 Chirality : 0.041 0.142 968 Planarity : 0.006 0.059 1070 Dihedral : 6.354 42.141 860 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.96 % Favored : 96.77 % Rotamer: Outliers : 3.61 % Allowed : 18.98 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.09 (0.31), residues: 742 helix: 2.25 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.64 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 607 HIS 0.006 0.001 HIS B 387 PHE 0.012 0.002 PHE B 517 TYR 0.017 0.002 TYR B 345 ARG 0.004 0.001 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 451) hydrogen bonds : angle 4.31412 ( 1353) covalent geometry : bond 0.00327 ( 6474) covalent geometry : angle 0.58486 ( 8810) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.723 Fit side-chains REVERT: A 543 GLU cc_start: 0.5062 (OUTLIER) cc_final: 0.4817 (mp0) REVERT: A 548 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7147 (ptt90) REVERT: B 543 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.4813 (mp0) REVERT: B 548 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7145 (ptt90) outliers start: 24 outliers final: 12 residues processed: 86 average time/residue: 1.4888 time to fit residues: 133.8026 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.199822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.187752 restraints weight = 4928.561| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 0.44 r_work: 0.3789 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6476 Z= 0.130 Angle : 0.513 5.723 8810 Z= 0.278 Chirality : 0.038 0.139 968 Planarity : 0.005 0.054 1070 Dihedral : 5.051 37.907 840 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 18.98 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.34 (0.31), residues: 742 helix: 2.35 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.49 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 607 HIS 0.002 0.001 HIS A 315 PHE 0.012 0.001 PHE B 460 TYR 0.009 0.001 TYR A 367 ARG 0.006 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 451) hydrogen bonds : angle 4.07899 ( 1353) covalent geometry : bond 0.00253 ( 6474) covalent geometry : angle 0.51285 ( 8810) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.943 Fit side-chains REVERT: A 543 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4845 (mp0) REVERT: B 543 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4843 (mp0) outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 1.5142 time to fit residues: 133.2024 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.197056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.185149 restraints weight = 4929.950| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 0.44 r_work: 0.3746 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6476 Z= 0.151 Angle : 0.552 8.796 8810 Z= 0.298 Chirality : 0.041 0.139 968 Planarity : 0.005 0.051 1070 Dihedral : 5.307 42.632 840 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.01 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.24 (0.31), residues: 742 helix: 2.28 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.55 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 514 HIS 0.002 0.001 HIS A 313 PHE 0.011 0.002 PHE B 610 TYR 0.018 0.002 TYR A 368 ARG 0.007 0.001 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 451) hydrogen bonds : angle 4.15361 ( 1353) covalent geometry : bond 0.00301 ( 6474) covalent geometry : angle 0.55236 ( 8810) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.605 Fit side-chains REVERT: A 543 GLU cc_start: 0.5227 (OUTLIER) cc_final: 0.4897 (mp0) REVERT: B 543 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.4892 (mp0) outliers start: 20 outliers final: 12 residues processed: 79 average time/residue: 1.3519 time to fit residues: 111.6195 Evaluate side-chains 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0804 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.193818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.183386 restraints weight = 4859.627| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 0.40 r_work: 0.3735 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6476 Z= 0.198 Angle : 0.632 8.318 8810 Z= 0.344 Chirality : 0.045 0.151 968 Planarity : 0.005 0.049 1070 Dihedral : 6.049 57.214 840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.52 % Allowed : 18.07 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.86 (0.31), residues: 742 helix: 2.01 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.75 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 514 HIS 0.003 0.001 HIS A 313 PHE 0.014 0.002 PHE B 394 TYR 0.020 0.002 TYR B 368 ARG 0.005 0.001 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.06554 ( 451) hydrogen bonds : angle 4.34913 ( 1353) covalent geometry : bond 0.00411 ( 6474) covalent geometry : angle 0.63227 ( 8810) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.688 Fit side-chains REVERT: A 543 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.4935 (mp0) REVERT: B 543 GLU cc_start: 0.5318 (OUTLIER) cc_final: 0.4939 (mp0) outliers start: 30 outliers final: 14 residues processed: 84 average time/residue: 1.1805 time to fit residues: 104.4673 Evaluate side-chains 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.197484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.186978 restraints weight = 4879.373| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 0.39 r_work: 0.3806 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6476 Z= 0.128 Angle : 0.514 7.208 8810 Z= 0.275 Chirality : 0.039 0.134 968 Planarity : 0.004 0.047 1070 Dihedral : 5.421 51.055 840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.28 (0.31), residues: 742 helix: 2.36 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.74 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 607 HIS 0.002 0.001 HIS B 616 PHE 0.013 0.001 PHE A 460 TYR 0.020 0.002 TYR A 368 ARG 0.005 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 451) hydrogen bonds : angle 4.05851 ( 1353) covalent geometry : bond 0.00261 ( 6474) covalent geometry : angle 0.51369 ( 8810) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.686 Fit side-chains REVERT: A 543 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4504 (mp0) REVERT: B 543 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4502 (mp0) outliers start: 20 outliers final: 6 residues processed: 84 average time/residue: 1.1850 time to fit residues: 104.7569 Evaluate side-chains 73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.196151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.185518 restraints weight = 4872.922| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 0.36 r_work: 0.3783 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6476 Z= 0.142 Angle : 0.533 7.029 8810 Z= 0.288 Chirality : 0.040 0.142 968 Planarity : 0.004 0.047 1070 Dihedral : 5.543 55.417 836 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.31 % Allowed : 19.28 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.33 (0.31), residues: 742 helix: 2.38 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.69 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 607 HIS 0.002 0.001 HIS B 313 PHE 0.012 0.002 PHE A 610 TYR 0.022 0.002 TYR A 368 ARG 0.004 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 451) hydrogen bonds : angle 4.12467 ( 1353) covalent geometry : bond 0.00289 ( 6474) covalent geometry : angle 0.53326 ( 8810) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.661 Fit side-chains REVERT: A 543 GLU cc_start: 0.5105 (OUTLIER) cc_final: 0.4543 (mp0) REVERT: B 543 GLU cc_start: 0.5106 (OUTLIER) cc_final: 0.4543 (mp0) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 1.2633 time to fit residues: 111.4557 Evaluate side-chains 75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.193659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.183034 restraints weight = 4762.159| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 0.36 r_work: 0.3769 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6476 Z= 0.178 Angle : 0.594 7.340 8810 Z= 0.323 Chirality : 0.044 0.147 968 Planarity : 0.005 0.047 1070 Dihedral : 5.756 51.362 836 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.01 % Allowed : 19.58 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.04 (0.31), residues: 742 helix: 2.14 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.69 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 514 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.002 PHE B 394 TYR 0.028 0.002 TYR A 368 ARG 0.004 0.001 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.06184 ( 451) hydrogen bonds : angle 4.29175 ( 1353) covalent geometry : bond 0.00370 ( 6474) covalent geometry : angle 0.59383 ( 8810) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 1.338 Fit side-chains REVERT: A 543 GLU cc_start: 0.5201 (OUTLIER) cc_final: 0.4618 (mp0) REVERT: B 543 GLU cc_start: 0.5196 (OUTLIER) cc_final: 0.4614 (mp0) outliers start: 20 outliers final: 12 residues processed: 75 average time/residue: 1.3663 time to fit residues: 108.3140 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.197622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.187566 restraints weight = 4873.645| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 0.38 r_work: 0.3801 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6476 Z= 0.128 Angle : 0.518 6.612 8810 Z= 0.277 Chirality : 0.039 0.140 968 Planarity : 0.004 0.045 1070 Dihedral : 5.443 51.642 836 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 19.58 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.39 (0.31), residues: 742 helix: 2.43 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 607 HIS 0.002 0.001 HIS A 313 PHE 0.013 0.001 PHE A 460 TYR 0.028 0.002 TYR A 368 ARG 0.004 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 451) hydrogen bonds : angle 4.08260 ( 1353) covalent geometry : bond 0.00254 ( 6474) covalent geometry : angle 0.51792 ( 8810) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.629 Fit side-chains REVERT: A 448 ARG cc_start: 0.7529 (ttt90) cc_final: 0.7327 (ttt90) REVERT: A 543 GLU cc_start: 0.5131 (OUTLIER) cc_final: 0.4522 (mp0) REVERT: B 448 ARG cc_start: 0.7525 (ttt90) cc_final: 0.7323 (ttt90) REVERT: B 543 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4522 (mp0) outliers start: 20 outliers final: 12 residues processed: 81 average time/residue: 1.3841 time to fit residues: 117.8352 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.195294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.186102 restraints weight = 4791.154| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 0.33 r_work: 0.3784 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6476 Z= 0.153 Angle : 0.557 6.900 8810 Z= 0.301 Chirality : 0.042 0.145 968 Planarity : 0.004 0.046 1070 Dihedral : 5.476 46.059 836 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.71 % Allowed : 19.73 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.24 (0.31), residues: 742 helix: 2.33 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.78 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 514 HIS 0.002 0.001 HIS B 315 PHE 0.011 0.002 PHE A 610 TYR 0.028 0.002 TYR A 368 ARG 0.003 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05628 ( 451) hydrogen bonds : angle 4.20213 ( 1353) covalent geometry : bond 0.00309 ( 6474) covalent geometry : angle 0.55743 ( 8810) Misc. bond : bond 0.00021 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.655 Fit side-chains REVERT: A 543 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4612 (mp0) REVERT: B 543 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.4612 (mp0) outliers start: 18 outliers final: 10 residues processed: 79 average time/residue: 1.2293 time to fit residues: 102.0048 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.195509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.186496 restraints weight = 4858.180| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 0.33 r_work: 0.3787 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6476 Z= 0.151 Angle : 0.556 6.842 8810 Z= 0.300 Chirality : 0.042 0.145 968 Planarity : 0.004 0.046 1070 Dihedral : 5.425 41.693 836 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.71 % Allowed : 19.88 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.20 (0.31), residues: 742 helix: 2.30 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.78 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 514 HIS 0.002 0.001 HIS A 315 PHE 0.012 0.002 PHE A 610 TYR 0.029 0.002 TYR B 368 ARG 0.004 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05602 ( 451) hydrogen bonds : angle 4.19989 ( 1353) covalent geometry : bond 0.00303 ( 6474) covalent geometry : angle 0.55636 ( 8810) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6628.02 seconds wall clock time: 117 minutes 48.90 seconds (7068.90 seconds total)