Starting phenix.real_space_refine on Thu Jul 24 15:13:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvs_27744/07_2025/8dvs_27744.cif" } resolution = 3.0 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 27 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3756 2.51 5 N 1038 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 6058 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5479 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 653} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4555 SG CYS A 810 42.435 21.036 29.261 1.00 21.81 S ATOM 4994 SG CYS A 864 42.810 19.059 25.632 1.00 25.59 S ATOM 5033 SG CYS A 869 39.720 20.716 26.736 1.00 33.77 S Time building chain proxies: 4.58, per 1000 atoms: 0.76 Number of scatterers: 6058 At special positions: 0 Unit cell: (91.92, 95.367, 68.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 27 15.00 Mg 1 11.99 O 1202 8.00 N 1038 7.00 C 3756 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: 1.60 Conformation dependent library (CDL) restraints added in 862.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 50.0% alpha, 7.9% beta 12 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.007A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.510A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 removed outlier: 3.990A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.632A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.845A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.653A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.943A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.056A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 4.393A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.858A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.750A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing helix chain 'A' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 6.548A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 462 removed outlier: 3.665A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.759A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 878 removed outlier: 3.660A pdb=" N VAL A 833 " --> pdb=" O PRO A 885 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 831 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 254 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1858 1.34 - 1.46: 1000 1.46 - 1.57: 3277 1.57 - 1.69: 52 1.69 - 1.81: 46 Bond restraints: 6233 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.15e-01 bond pdb=" CA ILE A 884 " pdb=" C ILE A 884 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.05e-02 9.07e+03 7.09e-01 bond pdb=" CA ILE A 704 " pdb=" CB ILE A 704 " ideal model delta sigma weight residual 1.551 1.542 0.009 1.08e-02 8.57e+03 6.62e-01 bond pdb=" CA GLN A 794 " pdb=" CB GLN A 794 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.31e-02 5.83e+03 5.77e-01 bond pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.30e-02 5.92e+03 4.09e-01 ... (remaining 6228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 8373 1.38 - 2.76: 132 2.76 - 4.14: 18 4.14 - 5.53: 10 5.53 - 6.91: 4 Bond angle restraints: 8537 Sorted by residual: angle pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta sigma weight residual 120.49 124.17 -3.68 1.38e+00 5.25e-01 7.11e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.81 110.08 1.73 8.60e-01 1.35e+00 4.06e+00 angle pdb=" CA LEU A 653 " pdb=" CB LEU A 653 " pdb=" CG LEU A 653 " ideal model delta sigma weight residual 116.30 123.21 -6.91 3.50e+00 8.16e-02 3.90e+00 angle pdb=" CA GLY A 413 " pdb=" C GLY A 413 " pdb=" O GLY A 413 " ideal model delta sigma weight residual 122.39 120.61 1.78 9.30e-01 1.16e+00 3.68e+00 angle pdb=" O1B ADP A1003 " pdb=" PB ADP A1003 " pdb=" O2B ADP A1003 " ideal model delta sigma weight residual 119.90 114.15 5.75 3.00e+00 1.11e-01 3.67e+00 ... (remaining 8532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 3606 25.17 - 50.35: 165 50.35 - 75.52: 52 75.52 - 100.70: 6 100.70 - 125.87: 3 Dihedral angle restraints: 3832 sinusoidal: 1830 harmonic: 2002 Sorted by residual: dihedral pdb=" C5' ADP A1003 " pdb=" O5' ADP A1003 " pdb=" PA ADP A1003 " pdb=" O2A ADP A1003 " ideal model delta sinusoidal sigma weight residual 300.00 174.13 125.87 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 47.56 -107.56 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" O1B ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PB ADP A1003 " pdb=" PA ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 46.73 -106.73 1 2.00e+01 2.50e-03 3.09e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 669 0.030 - 0.059: 197 0.059 - 0.089: 62 0.089 - 0.118: 40 0.118 - 0.148: 2 Chirality restraints: 970 Sorted by residual: chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 695 " pdb=" N ILE A 695 " pdb=" C ILE A 695 " pdb=" CB ILE A 695 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 967 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 382 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 300 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 301 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 884 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 885 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 885 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 885 " -0.014 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1514 2.80 - 3.32: 5449 3.32 - 3.85: 10363 3.85 - 4.37: 12130 4.37 - 4.90: 20246 Nonbonded interactions: 49702 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.271 3.120 nonbonded pdb=" OD2 ASP A 701 " pdb=" OH TYR A 717 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A 441 " pdb=" OE1 GLN A 769 " model vdw 2.316 3.040 nonbonded pdb=" O ASN A 625 " pdb=" OG1 THR A 628 " model vdw 2.324 3.040 nonbonded pdb=" OE1 GLN A 511 " pdb=" N2 G B 56 " model vdw 2.344 3.120 ... (remaining 49697 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.006 0.306 6236 Z= 0.210 Angle : 0.467 6.908 8537 Z= 0.259 Chirality : 0.036 0.148 970 Planarity : 0.003 0.027 997 Dihedral : 15.921 125.869 2532 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.32 % Allowed : 8.72 % Favored : 89.97 % 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: -1.94 (0.29), residues: 680 helix: 0.68 (0.27), residues: 300 sheet: -2.50 (0.44), residues: 112 loop : -3.08 (0.28), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 646 HIS 0.001 0.000 HIS A 375 PHE 0.007 0.001 PHE A 853 TYR 0.007 0.001 TYR A 246 ARG 0.001 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.12556 ( 285) hydrogen bonds : angle 4.20908 ( 803) metal coordination : bond 0.25848 ( 3) covalent geometry : bond 0.00156 ( 6233) covalent geometry : angle 0.46714 ( 8537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.652 Fit side-chains REVERT: A 425 ASP cc_start: 0.7298 (t0) cc_final: 0.6952 (t0) REVERT: A 510 GLU cc_start: 0.7944 (tt0) cc_final: 0.7741 (tt0) REVERT: A 593 LYS cc_start: 0.7826 (mttm) cc_final: 0.7467 (mtmm) REVERT: A 661 LEU cc_start: 0.8114 (tp) cc_final: 0.7885 (tp) REVERT: A 679 LYS cc_start: 0.7667 (tttt) cc_final: 0.6766 (tttt) REVERT: A 726 GLN cc_start: 0.7428 (mt0) cc_final: 0.7125 (mt0) REVERT: A 790 ILE cc_start: 0.8349 (mt) cc_final: 0.8092 (mp) REVERT: A 853 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6017 (p90) outliers start: 8 outliers final: 5 residues processed: 132 average time/residue: 1.2406 time to fit residues: 171.0745 Evaluate side-chains 88 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 306 GLN A 336 GLN A 341 ASN A 381 HIS A 419 ASN A 451 GLN A 457 GLN A 495 ASN A 517 GLN A 524 GLN A 584 GLN A 619 GLN A 668 ASN A 678 GLN A 708 GLN A 769 GLN A 830 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107221 restraints weight = 6186.495| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.69 r_work: 0.3098 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6236 Z= 0.120 Angle : 0.543 10.247 8537 Z= 0.256 Chirality : 0.040 0.220 970 Planarity : 0.003 0.034 997 Dihedral : 14.141 97.635 1147 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.12 % Allowed : 14.64 % Favored : 82.24 % 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 (0.31), residues: 680 helix: 1.65 (0.29), residues: 315 sheet: -2.37 (0.43), residues: 112 loop : -2.21 (0.32), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.002 0.001 HIS A 830 PHE 0.018 0.001 PHE A 853 TYR 0.019 0.001 TYR A 566 ARG 0.002 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 285) hydrogen bonds : angle 3.45748 ( 803) metal coordination : bond 0.00131 ( 3) covalent geometry : bond 0.00271 ( 6233) covalent geometry : angle 0.54319 ( 8537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.614 Fit side-chains REVERT: A 425 ASP cc_start: 0.8308 (t0) cc_final: 0.7888 (t0) REVERT: A 447 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 498 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: A 503 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7279 (mt-10) REVERT: A 593 LYS cc_start: 0.8158 (mttm) cc_final: 0.7692 (mttp) REVERT: A 595 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: A 673 MET cc_start: 0.8537 (ptp) cc_final: 0.8056 (ptp) REVERT: A 679 LYS cc_start: 0.7671 (tttt) cc_final: 0.6679 (tttt) REVERT: A 787 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 19 outliers final: 7 residues processed: 92 average time/residue: 1.3722 time to fit residues: 131.8286 Evaluate side-chains 79 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 39 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 317 HIS A 451 GLN A 457 GLN A 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.127400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.099505 restraints weight = 6288.518| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.83 r_work: 0.2831 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6236 Z= 0.163 Angle : 0.565 10.586 8537 Z= 0.272 Chirality : 0.042 0.177 970 Planarity : 0.004 0.038 997 Dihedral : 14.096 99.439 1143 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.11 % Allowed : 16.12 % Favored : 79.77 % 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: -0.29 (0.32), residues: 680 helix: 1.91 (0.30), residues: 315 sheet: -2.11 (0.45), residues: 110 loop : -2.04 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 771 HIS 0.003 0.001 HIS A 381 PHE 0.023 0.002 PHE A 853 TYR 0.016 0.002 TYR A 566 ARG 0.004 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 285) hydrogen bonds : angle 3.59631 ( 803) metal coordination : bond 0.00228 ( 3) covalent geometry : bond 0.00389 ( 6233) covalent geometry : angle 0.56546 ( 8537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.686 Fit side-chains REVERT: A 373 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 498 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: A 503 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7494 (mt-10) REVERT: A 593 LYS cc_start: 0.8178 (mttm) cc_final: 0.7459 (mttp) REVERT: A 595 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 613 ASP cc_start: 0.8131 (t0) cc_final: 0.7791 (t70) REVERT: A 653 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8029 (pp) REVERT: A 679 LYS cc_start: 0.7860 (tttt) cc_final: 0.6917 (tttm) REVERT: A 730 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7723 (ttm-80) REVERT: A 787 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 882 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.6780 (p90) outliers start: 25 outliers final: 11 residues processed: 86 average time/residue: 1.6846 time to fit residues: 151.1042 Evaluate side-chains 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101110 restraints weight = 6345.736| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.79 r_work: 0.2835 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6236 Z= 0.137 Angle : 0.540 9.997 8537 Z= 0.261 Chirality : 0.040 0.169 970 Planarity : 0.004 0.039 997 Dihedral : 14.062 99.235 1143 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.11 % Allowed : 16.12 % Favored : 79.77 % 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: 0.00 (0.32), residues: 680 helix: 2.12 (0.29), residues: 315 sheet: -2.02 (0.45), residues: 110 loop : -1.82 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.006 0.001 HIS A 317 PHE 0.022 0.001 PHE A 853 TYR 0.016 0.001 TYR A 566 ARG 0.006 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 285) hydrogen bonds : angle 3.51826 ( 803) metal coordination : bond 0.00183 ( 3) covalent geometry : bond 0.00322 ( 6233) covalent geometry : angle 0.53951 ( 8537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.677 Fit side-chains REVERT: A 447 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 470 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8147 (mttm) REVERT: A 498 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: A 503 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7508 (mt-10) REVERT: A 593 LYS cc_start: 0.8193 (mttm) cc_final: 0.7489 (mttp) REVERT: A 653 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7984 (pp) REVERT: A 664 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7778 (mpp-170) REVERT: A 679 LYS cc_start: 0.7835 (tttt) cc_final: 0.6877 (tttm) REVERT: A 730 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7648 (ttm-80) REVERT: A 882 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6908 (p90) outliers start: 25 outliers final: 12 residues processed: 86 average time/residue: 1.5972 time to fit residues: 143.0310 Evaluate side-chains 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.129493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101539 restraints weight = 6239.400| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.85 r_work: 0.2811 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6236 Z= 0.129 Angle : 0.531 9.640 8537 Z= 0.256 Chirality : 0.040 0.153 970 Planarity : 0.003 0.038 997 Dihedral : 14.044 102.620 1143 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.11 % Allowed : 17.43 % Favored : 78.45 % 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: 0.20 (0.33), residues: 680 helix: 2.27 (0.29), residues: 315 sheet: -2.00 (0.44), residues: 110 loop : -1.66 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 317 PHE 0.021 0.001 PHE A 853 TYR 0.015 0.001 TYR A 566 ARG 0.007 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 285) hydrogen bonds : angle 3.47795 ( 803) metal coordination : bond 0.00167 ( 3) covalent geometry : bond 0.00302 ( 6233) covalent geometry : angle 0.53110 ( 8537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.674 Fit side-chains REVERT: A 498 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: A 503 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7538 (mt-10) REVERT: A 510 GLU cc_start: 0.8570 (tt0) cc_final: 0.8359 (tt0) REVERT: A 593 LYS cc_start: 0.8242 (mttm) cc_final: 0.7505 (mttp) REVERT: A 595 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: A 653 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 664 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7909 (mpp-170) REVERT: A 679 LYS cc_start: 0.7877 (tttt) cc_final: 0.6934 (tttm) REVERT: A 730 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7691 (ttm-80) REVERT: A 882 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6915 (p90) outliers start: 25 outliers final: 12 residues processed: 83 average time/residue: 1.4195 time to fit residues: 122.7419 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.106632 restraints weight = 6163.081| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.72 r_work: 0.2818 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6236 Z= 0.112 Angle : 0.522 9.132 8537 Z= 0.250 Chirality : 0.039 0.147 970 Planarity : 0.003 0.037 997 Dihedral : 14.006 105.507 1143 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.62 % Allowed : 17.93 % Favored : 78.45 % 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: 0.32 (0.33), residues: 680 helix: 2.37 (0.29), residues: 315 sheet: -1.98 (0.44), residues: 110 loop : -1.57 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 381 PHE 0.019 0.001 PHE A 853 TYR 0.014 0.001 TYR A 566 ARG 0.007 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 285) hydrogen bonds : angle 3.44495 ( 803) metal coordination : bond 0.00127 ( 3) covalent geometry : bond 0.00258 ( 6233) covalent geometry : angle 0.52202 ( 8537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.670 Fit side-chains REVERT: A 498 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 503 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7407 (mt-10) REVERT: A 593 LYS cc_start: 0.8048 (mttm) cc_final: 0.7305 (mttp) REVERT: A 595 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: A 653 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7979 (pp) REVERT: A 664 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7784 (mpp-170) REVERT: A 679 LYS cc_start: 0.7673 (tttt) cc_final: 0.6687 (tttm) REVERT: A 730 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7075 (ttm-80) REVERT: A 882 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.6828 (p90) outliers start: 22 outliers final: 12 residues processed: 79 average time/residue: 1.3939 time to fit residues: 114.8929 Evaluate side-chains 78 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109777 restraints weight = 6170.731| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.74 r_work: 0.2940 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6236 Z= 0.105 Angle : 0.508 8.785 8537 Z= 0.244 Chirality : 0.039 0.142 970 Planarity : 0.003 0.036 997 Dihedral : 13.965 110.327 1143 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.61 % Allowed : 17.60 % Favored : 77.80 % 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: 0.41 (0.33), residues: 680 helix: 2.45 (0.29), residues: 315 sheet: -2.05 (0.43), residues: 112 loop : -1.48 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 PHE 0.017 0.001 PHE A 853 TYR 0.014 0.001 TYR A 566 ARG 0.005 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 285) hydrogen bonds : angle 3.39304 ( 803) metal coordination : bond 0.00119 ( 3) covalent geometry : bond 0.00238 ( 6233) covalent geometry : angle 0.50845 ( 8537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.659 Fit side-chains REVERT: A 498 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: A 503 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7487 (mt-10) REVERT: A 593 LYS cc_start: 0.8188 (mttm) cc_final: 0.7896 (mtpp) REVERT: A 595 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: A 653 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 679 LYS cc_start: 0.7832 (tttt) cc_final: 0.6873 (tttm) REVERT: A 730 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6970 (ttm-80) REVERT: A 767 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7587 (ttp-110) REVERT: A 882 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6896 (p90) outliers start: 28 outliers final: 15 residues processed: 84 average time/residue: 1.3108 time to fit residues: 115.1780 Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.135077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.106419 restraints weight = 6148.480| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.72 r_work: 0.2862 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6236 Z= 0.105 Angle : 0.516 8.585 8537 Z= 0.249 Chirality : 0.039 0.137 970 Planarity : 0.003 0.036 997 Dihedral : 13.938 112.840 1143 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.95 % Allowed : 18.42 % Favored : 77.63 % 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: 0.47 (0.33), residues: 680 helix: 2.50 (0.29), residues: 315 sheet: -2.00 (0.43), residues: 112 loop : -1.45 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 PHE 0.017 0.001 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.005 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 285) hydrogen bonds : angle 3.38494 ( 803) metal coordination : bond 0.00113 ( 3) covalent geometry : bond 0.00237 ( 6233) covalent geometry : angle 0.51618 ( 8537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.692 Fit side-chains REVERT: A 498 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: A 503 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7393 (mt-10) REVERT: A 591 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8110 (mp0) REVERT: A 593 LYS cc_start: 0.7987 (mttm) cc_final: 0.7681 (mtpp) REVERT: A 595 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: A 653 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7972 (pp) REVERT: A 679 LYS cc_start: 0.7655 (tttt) cc_final: 0.6658 (tttm) REVERT: A 730 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6888 (ttm-80) REVERT: A 767 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7475 (ttp-110) REVERT: A 787 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 882 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6828 (p90) outliers start: 24 outliers final: 16 residues processed: 83 average time/residue: 1.3893 time to fit residues: 120.6493 Evaluate side-chains 84 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.136044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108465 restraints weight = 6146.584| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.75 r_work: 0.2838 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6236 Z= 0.120 Angle : 0.538 9.268 8537 Z= 0.258 Chirality : 0.040 0.155 970 Planarity : 0.003 0.035 997 Dihedral : 13.964 116.817 1143 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.78 % Allowed : 18.59 % Favored : 77.63 % 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: 0.44 (0.33), residues: 680 helix: 2.47 (0.29), residues: 315 sheet: -2.08 (0.43), residues: 114 loop : -1.41 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 381 PHE 0.019 0.001 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.006 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 285) hydrogen bonds : angle 3.41251 ( 803) metal coordination : bond 0.00131 ( 3) covalent geometry : bond 0.00280 ( 6233) covalent geometry : angle 0.53843 ( 8537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.688 Fit side-chains REVERT: A 498 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: A 503 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7504 (mt-10) REVERT: A 593 LYS cc_start: 0.8133 (mttm) cc_final: 0.7831 (mtpp) REVERT: A 595 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: A 613 ASP cc_start: 0.8060 (t0) cc_final: 0.7748 (t0) REVERT: A 653 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8052 (pp) REVERT: A 679 LYS cc_start: 0.7837 (tttt) cc_final: 0.6878 (tttm) REVERT: A 730 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6992 (ttm-80) REVERT: A 767 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7573 (ttp-110) REVERT: A 787 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: A 882 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6959 (p90) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 2.0904 time to fit residues: 175.7063 Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102345 restraints weight = 6261.994| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.86 r_work: 0.2875 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6236 Z= 0.121 Angle : 0.539 8.867 8537 Z= 0.259 Chirality : 0.040 0.151 970 Planarity : 0.003 0.035 997 Dihedral : 13.959 119.958 1143 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.62 % Allowed : 18.75 % Favored : 77.63 % 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: 0.46 (0.33), residues: 680 helix: 2.48 (0.29), residues: 315 sheet: -2.07 (0.43), residues: 114 loop : -1.38 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.019 0.001 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.001 0.000 ARG A 845 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 285) hydrogen bonds : angle 3.42946 ( 803) metal coordination : bond 0.00148 ( 3) covalent geometry : bond 0.00280 ( 6233) covalent geometry : angle 0.53883 ( 8537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.850 Fit side-chains REVERT: A 498 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: A 503 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7549 (mt-10) REVERT: A 591 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8236 (mp0) REVERT: A 593 LYS cc_start: 0.8168 (mttm) cc_final: 0.7878 (mtpp) REVERT: A 595 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: A 613 ASP cc_start: 0.8103 (t0) cc_final: 0.7829 (t0) REVERT: A 653 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8076 (pp) REVERT: A 679 LYS cc_start: 0.7879 (tttt) cc_final: 0.6931 (tttm) REVERT: A 730 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7038 (ttm-80) REVERT: A 767 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7617 (ttp-110) REVERT: A 882 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7070 (p90) outliers start: 22 outliers final: 14 residues processed: 80 average time/residue: 1.9990 time to fit residues: 167.6753 Evaluate side-chains 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114614 restraints weight = 6246.043| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.67 r_work: 0.3069 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6236 Z= 0.091 Angle : 0.511 8.195 8537 Z= 0.244 Chirality : 0.038 0.158 970 Planarity : 0.003 0.036 997 Dihedral : 13.856 121.011 1143 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.80 % Allowed : 19.57 % Favored : 77.63 % 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: 0.61 (0.33), residues: 680 helix: 2.62 (0.29), residues: 315 sheet: -1.96 (0.43), residues: 112 loop : -1.36 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.001 0.000 HIS A 786 PHE 0.014 0.001 PHE A 853 TYR 0.012 0.001 TYR A 566 ARG 0.001 0.000 ARG A 791 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 285) hydrogen bonds : angle 3.30858 ( 803) metal coordination : bond 0.00076 ( 3) covalent geometry : bond 0.00197 ( 6233) covalent geometry : angle 0.51077 ( 8537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5247.90 seconds wall clock time: 94 minutes 36.37 seconds (5676.37 seconds total)