Starting phenix.real_space_refine on Tue Jul 29 00:45:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjw_38408/07_2025/8xjw_38408.cif" } resolution = 2.84 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= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5737 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 31 5.49 5 S 29 5.16 5 C 3882 2.51 5 N 1108 2.21 5 O 1197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 6248 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5595 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 666} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'DNA': 16} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 5.19, per 1000 atoms: 0.83 Number of scatterers: 6248 At special positions: 0 Unit cell: (73.186, 91.057, 107.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 29 16.00 P 31 15.00 O 1197 8.00 N 1108 7.00 C 3882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 697.3 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 35.7% alpha, 21.3% beta 9 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.789A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.557A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.693A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.561A pdb=" N THR A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.519A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.643A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.761A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.763A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 removed outlier: 3.696A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.363A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.730A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.935A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.817A pdb=" N THR A 639 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.666A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 382 removed outlier: 8.956A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 1318 1.45 - 1.57: 3290 1.57 - 1.69: 60 1.69 - 1.81: 51 Bond restraints: 6446 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.571 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CG1 ILE A 95 " pdb=" CD1 ILE A 95 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 bond pdb=" P DT B 1 " pdb=" OP2 DT B 1 " ideal model delta sigma weight residual 1.480 1.458 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta sigma weight residual 1.469 1.456 0.013 1.28e-02 6.10e+03 1.02e+00 bond pdb=" SD MET A 703 " pdb=" CE MET A 703 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.98e-01 ... (remaining 6441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8616 1.53 - 3.06: 196 3.06 - 4.59: 33 4.59 - 6.12: 6 6.12 - 7.65: 5 Bond angle restraints: 8856 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.30e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 111.91 105.62 6.29 8.90e-01 1.26e+00 4.99e+01 angle pdb=" CG1 ILE A 619 " pdb=" CB ILE A 619 " pdb=" CG2 ILE A 619 " ideal model delta sigma weight residual 110.70 103.31 7.39 3.00e+00 1.11e-01 6.07e+00 angle pdb=" C ASN A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta sigma weight residual 121.54 126.22 -4.68 1.91e+00 2.74e-01 6.00e+00 angle pdb=" C ILE A 457 " pdb=" N GLU A 458 " pdb=" CA GLU A 458 " ideal model delta sigma weight residual 120.72 116.87 3.85 1.67e+00 3.59e-01 5.32e+00 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 3584 27.64 - 55.27: 192 55.27 - 82.91: 30 82.91 - 110.54: 4 110.54 - 138.18: 1 Dihedral angle restraints: 3811 sinusoidal: 1776 harmonic: 2035 Sorted by residual: dihedral pdb=" CA ASN A 54 " pdb=" C ASN A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLN A 76 " pdb=" C GLN A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 764 0.043 - 0.087: 172 0.087 - 0.130: 57 0.130 - 0.173: 7 0.173 - 0.217: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CB ILE A 619 " pdb=" CA ILE A 619 " pdb=" CG1 ILE A 619 " pdb=" CG2 ILE A 619 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA GLN A 575 " pdb=" N GLN A 575 " pdb=" C GLN A 575 " pdb=" CB GLN A 575 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 999 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.029 2.00e-02 2.50e+03 1.48e-02 5.49e+00 pdb=" N1 DT B 1 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 49 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 50 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 705 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 706 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.019 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 158 2.69 - 3.24: 5711 3.24 - 3.79: 9694 3.79 - 4.35: 13469 4.35 - 4.90: 21861 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" CG1 VAL A 737 " pdb="MN MN A 801 " model vdw 2.132 2.740 nonbonded pdb=" OE1 GLN A 510 " pdb=" OG1 THR A 732 " model vdw 2.241 3.040 nonbonded pdb=" NZ LYS A 269 " pdb=" O2 DT B 6 " model vdw 2.248 3.120 nonbonded pdb=" OE1 GLN A 435 " pdb=" NE2 GLN A 723 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 434 " pdb=" OP3 DT B 1 " model vdw 2.277 3.040 ... (remaining 50888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 165.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:35.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.003 0.091 6446 Z= 0.132 Angle : 0.579 7.646 8856 Z= 0.325 Chirality : 0.042 0.217 1002 Planarity : 0.004 0.040 1013 Dihedral : 16.621 138.177 2495 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.92 (0.32), residues: 684 helix: 0.12 (0.34), residues: 239 sheet: 0.48 (0.42), residues: 151 loop : -1.83 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.14211 ( 254) hydrogen bonds : angle 7.12257 ( 725) covalent geometry : bond 0.00276 ( 6446) covalent geometry : angle 0.57949 ( 8856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.4887 (mtt) cc_final: 0.4602 (mtm) REVERT: A 493 TYR cc_start: 0.6802 (t80) cc_final: 0.6548 (t80) REVERT: A 667 MET cc_start: 0.7941 (ttt) cc_final: 0.7643 (ttt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 1.3543 time to fit residues: 142.4841 Evaluate side-chains 73 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 126 GLN A 257 GLN A 379 ASN A 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.208626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165297 restraints weight = 6257.134| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.71 r_work: 0.3672 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6446 Z= 0.211 Angle : 0.703 7.809 8856 Z= 0.369 Chirality : 0.047 0.170 1002 Planarity : 0.004 0.042 1013 Dihedral : 16.756 134.961 1140 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.13 % Allowed : 10.74 % Favored : 85.12 % 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: -1.02 (0.31), residues: 684 helix: 0.17 (0.33), residues: 243 sheet: 0.27 (0.42), residues: 154 loop : -1.97 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 282 HIS 0.004 0.001 HIS A 356 PHE 0.017 0.002 PHE A 253 TYR 0.017 0.002 TYR A 307 ARG 0.005 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.05405 ( 254) hydrogen bonds : angle 5.33995 ( 725) covalent geometry : bond 0.00490 ( 6446) covalent geometry : angle 0.70260 ( 8856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.664 Fit side-chains REVERT: A 38 HIS cc_start: 0.6479 (OUTLIER) cc_final: 0.5808 (p90) REVERT: A 163 MET cc_start: 0.5503 (mtt) cc_final: 0.4913 (mtm) REVERT: A 259 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 439 GLN cc_start: 0.6617 (mt0) cc_final: 0.6235 (mt0) outliers start: 25 outliers final: 6 residues processed: 92 average time/residue: 1.3741 time to fit residues: 134.0299 Evaluate side-chains 84 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 615 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 379 ASN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.211869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.181670 restraints weight = 6280.984| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.09 r_work: 0.3689 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6446 Z= 0.122 Angle : 0.590 7.861 8856 Z= 0.313 Chirality : 0.043 0.166 1002 Planarity : 0.004 0.033 1013 Dihedral : 16.598 135.087 1140 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.14 % Allowed : 14.88 % Favored : 81.98 % 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: -0.77 (0.31), residues: 684 helix: 0.46 (0.34), residues: 240 sheet: 0.51 (0.41), residues: 154 loop : -1.95 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 282 HIS 0.003 0.001 HIS A 581 PHE 0.011 0.001 PHE A 319 TYR 0.007 0.001 TYR A 363 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 254) hydrogen bonds : angle 4.88263 ( 725) covalent geometry : bond 0.00267 ( 6446) covalent geometry : angle 0.58971 ( 8856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.5813 (p90) REVERT: A 163 MET cc_start: 0.5716 (mtt) cc_final: 0.5221 (mtm) REVERT: A 259 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: A 415 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.7079 (p) REVERT: A 615 ILE cc_start: 0.5524 (mt) cc_final: 0.5150 (mt) outliers start: 19 outliers final: 7 residues processed: 99 average time/residue: 1.1467 time to fit residues: 120.4892 Evaluate side-chains 86 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 257 GLN A 379 ASN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.209957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.179869 restraints weight = 6366.592| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.11 r_work: 0.3661 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6446 Z= 0.142 Angle : 0.617 7.518 8856 Z= 0.324 Chirality : 0.044 0.174 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.586 135.519 1140 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.81 % Allowed : 18.02 % Favored : 79.17 % 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: -0.65 (0.32), residues: 684 helix: 0.56 (0.34), residues: 240 sheet: 0.71 (0.41), residues: 157 loop : -2.01 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.009 0.001 PHE A 319 TYR 0.010 0.001 TYR A 307 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 254) hydrogen bonds : angle 4.79755 ( 725) covalent geometry : bond 0.00320 ( 6446) covalent geometry : angle 0.61710 ( 8856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.5790 (p90) REVERT: A 163 MET cc_start: 0.5633 (mtt) cc_final: 0.5224 (mtm) REVERT: A 165 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7271 (pp20) REVERT: A 259 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 615 ILE cc_start: 0.5608 (mt) cc_final: 0.5200 (mt) outliers start: 17 outliers final: 6 residues processed: 88 average time/residue: 1.4947 time to fit residues: 138.5250 Evaluate side-chains 83 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 0.0040 chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 638 ASN A 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.209732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.167451 restraints weight = 6316.895| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.97 r_work: 0.3645 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6446 Z= 0.182 Angle : 0.663 8.019 8856 Z= 0.346 Chirality : 0.045 0.177 1002 Planarity : 0.004 0.032 1013 Dihedral : 16.682 136.122 1140 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.46 % Allowed : 18.84 % Favored : 76.69 % 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: -0.75 (0.32), residues: 684 helix: 0.51 (0.34), residues: 239 sheet: 0.62 (0.41), residues: 157 loop : -2.06 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.005 0.001 HIS A 710 PHE 0.011 0.002 PHE A 319 TYR 0.015 0.001 TYR A 307 ARG 0.003 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 254) hydrogen bonds : angle 4.91854 ( 725) covalent geometry : bond 0.00419 ( 6446) covalent geometry : angle 0.66306 ( 8856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.5866 (p90) REVERT: A 55 GLN cc_start: 0.7227 (tt0) cc_final: 0.6721 (tp40) REVERT: A 163 MET cc_start: 0.5595 (mtt) cc_final: 0.5156 (mtm) REVERT: A 185 TYR cc_start: 0.5244 (m-10) cc_final: 0.4984 (m-80) REVERT: A 259 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: A 291 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7193 (mmp80) REVERT: A 615 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5217 (mt) outliers start: 27 outliers final: 10 residues processed: 91 average time/residue: 1.2861 time to fit residues: 124.6944 Evaluate side-chains 87 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 311 GLN A 379 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.209494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.167422 restraints weight = 6299.291| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.99 r_work: 0.3638 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6446 Z= 0.192 Angle : 0.679 8.569 8856 Z= 0.354 Chirality : 0.045 0.184 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.706 135.875 1140 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.30 % Allowed : 20.66 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.31), residues: 684 helix: 0.45 (0.34), residues: 239 sheet: 0.57 (0.41), residues: 157 loop : -2.10 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 282 HIS 0.005 0.001 HIS A 710 PHE 0.018 0.002 PHE A 319 TYR 0.017 0.002 TYR A 307 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 254) hydrogen bonds : angle 4.94487 ( 725) covalent geometry : bond 0.00445 ( 6446) covalent geometry : angle 0.67940 ( 8856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.5837 (p90) REVERT: A 55 GLN cc_start: 0.7214 (tt0) cc_final: 0.6745 (tp40) REVERT: A 163 MET cc_start: 0.5734 (mtt) cc_final: 0.5137 (mtm) REVERT: A 175 ARG cc_start: 0.5906 (ttm170) cc_final: 0.5367 (ttt90) REVERT: A 185 TYR cc_start: 0.5248 (m-10) cc_final: 0.4998 (m-80) REVERT: A 259 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: A 291 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7276 (mmp80) REVERT: A 311 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: A 615 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5213 (mt) outliers start: 26 outliers final: 12 residues processed: 91 average time/residue: 1.3798 time to fit residues: 134.5011 Evaluate side-chains 91 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.0270 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 379 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.209227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166717 restraints weight = 6308.069| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 3.01 r_work: 0.3662 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6446 Z= 0.159 Angle : 0.646 8.735 8856 Z= 0.338 Chirality : 0.044 0.196 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.656 135.227 1140 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.97 % Allowed : 21.16 % Favored : 74.88 % 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: -0.77 (0.31), residues: 684 helix: 0.54 (0.34), residues: 239 sheet: 0.61 (0.41), residues: 157 loop : -2.11 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.014 0.001 PHE A 319 TYR 0.014 0.001 TYR A 307 ARG 0.003 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 254) hydrogen bonds : angle 4.88917 ( 725) covalent geometry : bond 0.00365 ( 6446) covalent geometry : angle 0.64576 ( 8856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5829 (p90) REVERT: A 55 GLN cc_start: 0.7215 (tt0) cc_final: 0.6777 (tp40) REVERT: A 163 MET cc_start: 0.5765 (mtt) cc_final: 0.5182 (mtm) REVERT: A 175 ARG cc_start: 0.6024 (ttt180) cc_final: 0.5592 (ttt90) REVERT: A 185 TYR cc_start: 0.5231 (m-10) cc_final: 0.4989 (m-80) REVERT: A 259 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: A 311 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: A 615 ILE cc_start: 0.5560 (OUTLIER) cc_final: 0.5098 (mt) outliers start: 24 outliers final: 10 residues processed: 90 average time/residue: 2.0745 time to fit residues: 200.4169 Evaluate side-chains 89 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 638 ASN A 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.211168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181769 restraints weight = 6305.785| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.07 r_work: 0.3676 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6446 Z= 0.130 Angle : 0.621 9.442 8856 Z= 0.326 Chirality : 0.044 0.210 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.576 134.559 1140 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.98 % Allowed : 22.48 % Favored : 74.55 % 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: -0.64 (0.32), residues: 684 helix: 0.63 (0.35), residues: 239 sheet: 0.74 (0.41), residues: 157 loop : -2.08 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 PHE 0.012 0.001 PHE A 319 TYR 0.011 0.001 TYR A 307 ARG 0.002 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 254) hydrogen bonds : angle 4.78912 ( 725) covalent geometry : bond 0.00290 ( 6446) covalent geometry : angle 0.62119 ( 8856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.5817 (p90) REVERT: A 55 GLN cc_start: 0.7213 (tt0) cc_final: 0.6785 (tp40) REVERT: A 163 MET cc_start: 0.5811 (mtt) cc_final: 0.5329 (mtm) REVERT: A 185 TYR cc_start: 0.5155 (m-10) cc_final: 0.4947 (m-80) REVERT: A 259 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: A 291 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7316 (mmp80) REVERT: A 667 MET cc_start: 0.8140 (ttt) cc_final: 0.7748 (ttt) outliers start: 18 outliers final: 11 residues processed: 87 average time/residue: 1.3546 time to fit residues: 124.9749 Evaluate side-chains 91 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 311 GLN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.214101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171822 restraints weight = 6349.730| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.87 r_work: 0.3759 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6446 Z= 0.114 Angle : 0.611 11.007 8856 Z= 0.321 Chirality : 0.043 0.215 1002 Planarity : 0.003 0.029 1013 Dihedral : 16.520 134.144 1140 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.48 % Allowed : 23.31 % Favored : 74.21 % 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: -0.57 (0.32), residues: 684 helix: 0.82 (0.36), residues: 229 sheet: 0.82 (0.41), residues: 157 loop : -2.09 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 590 PHE 0.024 0.001 PHE A 319 TYR 0.006 0.001 TYR A 323 ARG 0.002 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 254) hydrogen bonds : angle 4.71528 ( 725) covalent geometry : bond 0.00248 ( 6446) covalent geometry : angle 0.61096 ( 8856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5868 (p90) REVERT: A 55 GLN cc_start: 0.7138 (tt0) cc_final: 0.6708 (tp40) REVERT: A 67 MET cc_start: 0.6677 (tpt) cc_final: 0.6196 (tpt) REVERT: A 163 MET cc_start: 0.5777 (mtt) cc_final: 0.5272 (mtm) REVERT: A 177 VAL cc_start: 0.5954 (p) cc_final: 0.5713 (m) REVERT: A 185 TYR cc_start: 0.5082 (m-10) cc_final: 0.4869 (m-80) REVERT: A 291 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7208 (mmp80) REVERT: A 311 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7307 (mm-40) REVERT: A 458 GLU cc_start: 0.7099 (mp0) cc_final: 0.6653 (tp30) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 1.1434 time to fit residues: 115.7733 Evaluate side-chains 91 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 638 ASN A 644 GLN A 674 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.211015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.168714 restraints weight = 6378.075| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.98 r_work: 0.3665 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6446 Z= 0.177 Angle : 0.695 10.841 8856 Z= 0.362 Chirality : 0.046 0.226 1002 Planarity : 0.004 0.034 1013 Dihedral : 16.630 135.902 1140 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 2.48 % Allowed : 23.14 % Favored : 74.38 % 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: -0.73 (0.32), residues: 684 helix: 0.66 (0.36), residues: 229 sheet: 0.71 (0.42), residues: 157 loop : -2.14 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.028 0.002 PHE A 319 TYR 0.019 0.001 TYR A 307 ARG 0.007 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 254) hydrogen bonds : angle 4.99356 ( 725) covalent geometry : bond 0.00408 ( 6446) covalent geometry : angle 0.69537 ( 8856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.5835 (p90) REVERT: A 55 GLN cc_start: 0.7266 (tt0) cc_final: 0.6911 (tp40) REVERT: A 163 MET cc_start: 0.5618 (mtt) cc_final: 0.5063 (mtm) REVERT: A 185 TYR cc_start: 0.5223 (m-10) cc_final: 0.4987 (m-80) REVERT: A 259 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: A 291 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7329 (mmp80) REVERT: A 311 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: A 458 GLU cc_start: 0.7138 (mp0) cc_final: 0.6703 (tp30) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 1.0211 time to fit residues: 94.2850 Evaluate side-chains 90 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 638 ASN A 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.213266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.171711 restraints weight = 6440.083| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.93 r_work: 0.3689 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6446 Z= 0.141 Angle : 0.667 13.243 8856 Z= 0.349 Chirality : 0.045 0.223 1002 Planarity : 0.004 0.034 1013 Dihedral : 16.571 134.717 1140 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.42 % Rotamer: Outliers : 2.31 % Allowed : 23.31 % Favored : 74.38 % 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: -0.67 (0.32), residues: 684 helix: 0.72 (0.36), residues: 229 sheet: 0.73 (0.41), residues: 157 loop : -2.12 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 282 HIS 0.005 0.001 HIS A 581 PHE 0.027 0.001 PHE A 319 TYR 0.011 0.001 TYR A 307 ARG 0.014 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 254) hydrogen bonds : angle 4.88937 ( 725) covalent geometry : bond 0.00319 ( 6446) covalent geometry : angle 0.66733 ( 8856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5963.07 seconds wall clock time: 112 minutes 9.71 seconds (6729.71 seconds total)