Starting phenix.real_space_refine on Wed Sep 17 19:42:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjw_38408/09_2025/8xjw_38408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjw_38408/09_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_38408/09_2025/8xjw_38408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjw_38408/09_2025/8xjw_38408.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjw_38408/09_2025/8xjw_38408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjw_38408/09_2025/8xjw_38408.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, '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: 1.83, per 1000 atoms: 0.29 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: 0.59 Conformation dependent library (CDL) restraints added in 336.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.85 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: 1.27 Time building geometry restraints manager: 0.77 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 275 TYR 0.008 0.001 TYR A 363 PHE 0.010 0.001 PHE A 86 TRP 0.013 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6446) covalent geometry : angle 0.57949 ( 8856) hydrogen bonds : bond 0.14211 ( 254) hydrogen bonds : angle 7.12257 ( 725) *********************** 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 : 0.232 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.4887 (mtt) cc_final: 0.4604 (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: 0.7642 (ttt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.5695 time to fit residues: 59.9387 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 : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 A 674 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171967 restraints weight = 6315.317| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.38 r_work: 0.3643 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1344 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= 0.155 Angle : 0.639 7.571 8856 Z= 0.337 Chirality : 0.045 0.185 1002 Planarity : 0.004 0.036 1013 Dihedral : 16.587 133.724 1140 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.98 % Allowed : 10.91 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.31), residues: 684 helix: 0.39 (0.34), residues: 242 sheet: 0.43 (0.42), residues: 154 loop : -1.90 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.013 0.001 TYR A 307 PHE 0.014 0.002 PHE A 492 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6446) covalent geometry : angle 0.63949 ( 8856) hydrogen bonds : bond 0.04902 ( 254) hydrogen bonds : angle 5.19744 ( 725) *********************** 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 97 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.244 Fit side-chains REVERT: A 38 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.5822 (p90) REVERT: A 163 MET cc_start: 0.5680 (mtt) cc_final: 0.5147 (mtm) REVERT: A 259 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: A 291 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7230 (mmp-170) REVERT: A 439 GLN cc_start: 0.6614 (mt0) cc_final: 0.6265 (mt0) outliers start: 18 outliers final: 5 residues processed: 89 average time/residue: 0.5887 time to fit residues: 55.1406 Evaluate side-chains 86 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG 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 671 ILE Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.209311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166722 restraints weight = 6270.662| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.87 r_work: 0.3695 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6446 Z= 0.159 Angle : 0.633 7.304 8856 Z= 0.332 Chirality : 0.044 0.167 1002 Planarity : 0.004 0.035 1013 Dihedral : 16.632 136.448 1140 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.64 % Allowed : 14.55 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.31), residues: 684 helix: 0.44 (0.34), residues: 240 sheet: 0.50 (0.41), residues: 154 loop : -2.00 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.012 0.001 TYR A 307 PHE 0.013 0.002 PHE A 319 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6446) covalent geometry : angle 0.63329 ( 8856) hydrogen bonds : bond 0.04724 ( 254) hydrogen bonds : angle 4.98077 ( 725) *********************** 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 103 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.5793 (p90) REVERT: A 163 MET cc_start: 0.5568 (mtt) cc_final: 0.5130 (mtm) REVERT: A 259 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 415 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 615 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5177 (mt) outliers start: 22 outliers final: 6 residues processed: 94 average time/residue: 0.5137 time to fit residues: 51.2288 Evaluate side-chains 85 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 294 THR 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 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.208157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.165963 restraints weight = 6336.376| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.92 r_work: 0.3637 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6446 Z= 0.182 Angle : 0.666 7.584 8856 Z= 0.348 Chirality : 0.045 0.174 1002 Planarity : 0.004 0.032 1013 Dihedral : 16.677 135.981 1140 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.64 % Allowed : 16.69 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.31), residues: 684 helix: 0.40 (0.34), residues: 240 sheet: 0.59 (0.41), residues: 152 loop : -2.06 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.015 0.001 TYR A 307 PHE 0.012 0.002 PHE A 319 TRP 0.012 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6446) covalent geometry : angle 0.66569 ( 8856) hydrogen bonds : bond 0.04812 ( 254) hydrogen bonds : angle 4.97988 ( 725) *********************** 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 103 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.5826 (p90) REVERT: A 163 MET cc_start: 0.5540 (mtt) cc_final: 0.5105 (mtm) REVERT: A 259 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 493 TYR cc_start: 0.7524 (t80) cc_final: 0.7300 (t80) REVERT: A 615 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5248 (mt) outliers start: 22 outliers final: 9 residues processed: 94 average time/residue: 0.5692 time to fit residues: 56.4543 Evaluate side-chains 89 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 294 THR 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 615 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.0980 chunk 68 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN 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 = 0.4505 r_free = 0.4505 target = 0.214038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.184914 restraints weight = 6454.128| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.06 r_work: 0.3715 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6446 Z= 0.107 Angle : 0.577 8.130 8856 Z= 0.306 Chirality : 0.043 0.179 1002 Planarity : 0.003 0.030 1013 Dihedral : 16.510 134.063 1140 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.64 % Allowed : 20.33 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.32), residues: 684 helix: 0.73 (0.34), residues: 238 sheet: 0.84 (0.41), residues: 157 loop : -1.99 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.006 0.001 TYR A 363 PHE 0.011 0.001 PHE A 319 TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6446) covalent geometry : angle 0.57703 ( 8856) hydrogen bonds : bond 0.04268 ( 254) hydrogen bonds : angle 4.69086 ( 725) *********************** 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 103 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.5785 (p90) REVERT: A 55 GLN cc_start: 0.7137 (tt0) cc_final: 0.6619 (tp40) REVERT: A 163 MET cc_start: 0.5689 (mtt) cc_final: 0.5281 (mtm) REVERT: A 259 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 458 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6875 (tm-30) REVERT: A 615 ILE cc_start: 0.5484 (mt) cc_final: 0.5104 (mt) outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 0.5055 time to fit residues: 50.4232 Evaluate side-chains 87 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 549 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN A 638 ASN A 644 GLN A 710 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.206968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164896 restraints weight = 6340.582| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.96 r_work: 0.3635 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6446 Z= 0.212 Angle : 0.701 8.169 8856 Z= 0.364 Chirality : 0.046 0.190 1002 Planarity : 0.004 0.032 1013 Dihedral : 16.728 136.624 1140 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.47 % Allowed : 20.66 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.31), residues: 684 helix: 0.46 (0.34), residues: 240 sheet: 0.64 (0.41), residues: 157 loop : -2.15 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.019 0.002 TYR A 307 PHE 0.018 0.002 PHE A 319 TRP 0.010 0.002 TRP A 282 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6446) covalent geometry : angle 0.70061 ( 8856) hydrogen bonds : bond 0.04966 ( 254) hydrogen bonds : angle 4.98763 ( 725) *********************** 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 96 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6528 (OUTLIER) cc_final: 0.5875 (p90) REVERT: A 55 GLN cc_start: 0.7246 (tt0) cc_final: 0.6754 (tp40) REVERT: A 163 MET cc_start: 0.5676 (mtt) cc_final: 0.5064 (mtm) REVERT: A 185 TYR cc_start: 0.5258 (m-10) cc_final: 0.5015 (m-80) REVERT: A 259 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: A 493 TYR cc_start: 0.7530 (t80) cc_final: 0.7300 (t80) REVERT: A 615 ILE cc_start: 0.5715 (mt) cc_final: 0.5260 (mt) outliers start: 21 outliers final: 9 residues processed: 87 average time/residue: 0.5499 time to fit residues: 50.5474 Evaluate side-chains 84 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 575 GLN Chi-restraints excluded: chain A residue 576 MET 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 23 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 60 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.209487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167332 restraints weight = 6312.816| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.90 r_work: 0.3672 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2105 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= 0.144 Angle : 0.642 8.794 8856 Z= 0.335 Chirality : 0.044 0.193 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.623 135.094 1140 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.64 % Allowed : 21.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.31), residues: 684 helix: 0.60 (0.34), residues: 237 sheet: 0.70 (0.41), residues: 157 loop : -2.12 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 275 TYR 0.010 0.001 TYR A 307 PHE 0.013 0.001 PHE A 319 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6446) covalent geometry : angle 0.64246 ( 8856) hydrogen bonds : bond 0.04428 ( 254) hydrogen bonds : angle 4.87631 ( 725) *********************** 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 96 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.5838 (p90) REVERT: A 55 GLN cc_start: 0.7231 (tt0) cc_final: 0.6768 (tp40) REVERT: A 163 MET cc_start: 0.5766 (mtt) cc_final: 0.5199 (mtm) REVERT: A 185 TYR cc_start: 0.5228 (m-10) cc_final: 0.4990 (m-80) REVERT: A 259 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: A 291 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7303 (mmp80) REVERT: A 311 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: A 615 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5222 (mt) outliers start: 22 outliers final: 8 residues processed: 89 average time/residue: 0.5212 time to fit residues: 49.0792 Evaluate side-chains 87 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG 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 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 703 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.209213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.167397 restraints weight = 6352.435| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.98 r_work: 0.3652 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6446 Z= 0.156 Angle : 0.664 9.304 8856 Z= 0.347 Chirality : 0.045 0.208 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.629 135.165 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 : 3.31 % Allowed : 21.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.31), residues: 684 helix: 0.52 (0.34), residues: 237 sheet: 0.68 (0.41), residues: 157 loop : -2.15 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.015 0.001 TYR A 307 PHE 0.011 0.001 PHE A 319 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6446) covalent geometry : angle 0.66392 ( 8856) hydrogen bonds : bond 0.04488 ( 254) hydrogen bonds : angle 4.97488 ( 725) *********************** 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 92 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.5826 (p90) REVERT: A 55 GLN cc_start: 0.7322 (tt0) cc_final: 0.6863 (tp40) REVERT: A 67 MET cc_start: 0.6854 (tpt) cc_final: 0.6536 (tpt) REVERT: A 163 MET cc_start: 0.5751 (mtt) cc_final: 0.5190 (mtm) REVERT: A 185 TYR cc_start: 0.5216 (m-10) cc_final: 0.4990 (m-80) REVERT: A 259 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 311 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: A 615 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.4220 (mt) outliers start: 20 outliers final: 11 residues processed: 84 average time/residue: 0.5236 time to fit residues: 46.6139 Evaluate side-chains 87 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain A residue 264 VAL 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 Chi-restraints excluded: chain A residue 703 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN A 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.211783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169353 restraints weight = 6405.220| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.85 r_work: 0.3731 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6446 Z= 0.121 Angle : 0.629 10.791 8856 Z= 0.330 Chirality : 0.044 0.215 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.545 134.281 1140 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.64 % Allowed : 22.64 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.32), residues: 684 helix: 0.65 (0.35), residues: 231 sheet: 0.81 (0.41), residues: 157 loop : -2.06 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 643 TYR 0.007 0.001 TYR A 307 PHE 0.008 0.001 PHE A 86 TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6446) covalent geometry : angle 0.62936 ( 8856) hydrogen bonds : bond 0.04208 ( 254) hydrogen bonds : angle 4.92312 ( 725) *********************** 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 95 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.5824 (p90) REVERT: A 55 GLN cc_start: 0.7225 (tt0) cc_final: 0.6781 (tp40) REVERT: A 67 MET cc_start: 0.6747 (tpt) cc_final: 0.6495 (tpt) REVERT: A 163 MET cc_start: 0.5793 (mtt) cc_final: 0.5312 (mtm) REVERT: A 185 TYR cc_start: 0.5163 (m-10) cc_final: 0.4931 (m-80) REVERT: A 291 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7306 (mmp80) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.5433 time to fit residues: 50.5644 Evaluate side-chains 86 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS 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 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 Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 703 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.212349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.170018 restraints weight = 6325.562| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.86 r_work: 0.3735 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6446 Z= 0.122 Angle : 0.633 10.938 8856 Z= 0.330 Chirality : 0.044 0.226 1002 Planarity : 0.004 0.033 1013 Dihedral : 16.506 134.288 1140 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.98 % Allowed : 21.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.32), residues: 684 helix: 0.62 (0.35), residues: 232 sheet: 0.90 (0.41), residues: 157 loop : -2.00 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR A 307 PHE 0.013 0.001 PHE A 61 TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6446) covalent geometry : angle 0.63279 ( 8856) hydrogen bonds : bond 0.04130 ( 254) hydrogen bonds : angle 4.93874 ( 725) ********************** 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 96 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.5788 (p90) REVERT: A 55 GLN cc_start: 0.7276 (tt0) cc_final: 0.6819 (tp40) REVERT: A 163 MET cc_start: 0.5657 (mtt) cc_final: 0.5260 (mtm) REVERT: A 185 TYR cc_start: 0.5139 (m-10) cc_final: 0.4915 (m-80) REVERT: A 259 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6659 (tt0) REVERT: A 311 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7294 (mm-40) outliers start: 18 outliers final: 11 residues processed: 87 average time/residue: 0.5415 time to fit residues: 49.8452 Evaluate side-chains 92 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain A residue 264 VAL 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 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 Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 703 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.212231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.170113 restraints weight = 6394.609| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.80 r_work: 0.3726 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6446 Z= 0.135 Angle : 0.658 13.082 8856 Z= 0.341 Chirality : 0.044 0.228 1002 Planarity : 0.004 0.030 1013 Dihedral : 16.514 134.531 1140 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.31 % Allowed : 22.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.32), residues: 684 helix: 0.69 (0.35), residues: 230 sheet: 0.84 (0.41), residues: 157 loop : -2.01 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.010 0.001 TYR A 307 PHE 0.011 0.001 PHE A 61 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6446) covalent geometry : angle 0.65771 ( 8856) hydrogen bonds : bond 0.04177 ( 254) hydrogen bonds : angle 4.87480 ( 725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.89 seconds wall clock time: 42 minutes 35.81 seconds (2555.81 seconds total)