Starting phenix.real_space_refine on Fri Aug 22 17:17:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvs_27744/08_2025/8dvs_27744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvs_27744/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dvs_27744/08_2025/8dvs_27744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvs_27744/08_2025/8dvs_27744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dvs_27744/08_2025/8dvs_27744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvs_27744/08_2025/8dvs_27744.map" } resolution = 3.0 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= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.48, per 1000 atoms: 0.24 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: 0.39 Conformation dependent library (CDL) restraints added in 285.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 0.75 Time building geometry restraints manager: 0.50 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.340 Find NCS groups from input model: 0.020 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.001 0.000 ARG A 734 TYR 0.007 0.001 TYR A 246 PHE 0.007 0.001 PHE A 853 TRP 0.001 0.000 TRP A 646 HIS 0.001 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00156 ( 6233) covalent geometry : angle 0.46714 ( 8537) hydrogen bonds : bond 0.12556 ( 285) hydrogen bonds : angle 4.20908 ( 803) metal coordination : bond 0.25848 ( 3) *********************** 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 : 0.181 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: 0.5467 time to fit residues: 75.1991 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 : 0.168 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 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 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 = 0.3422 r_free = 0.3422 target = 0.136193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.108942 restraints weight = 6248.918| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.58 r_work: 0.3054 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6236 Z= 0.118 Angle : 0.530 10.164 8537 Z= 0.249 Chirality : 0.040 0.218 970 Planarity : 0.003 0.034 997 Dihedral : 14.186 99.541 1147 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.80 % Allowed : 14.47 % Favored : 82.73 % 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: -0.61 (0.31), residues: 680 helix: 1.80 (0.29), residues: 309 sheet: -2.23 (0.42), residues: 122 loop : -2.32 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.018 0.001 TYR A 566 PHE 0.017 0.001 PHE A 853 TRP 0.006 0.001 TRP A 908 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6233) covalent geometry : angle 0.53044 ( 8537) hydrogen bonds : bond 0.03642 ( 285) hydrogen bonds : angle 3.44878 ( 803) metal coordination : bond 0.01097 ( 3) *********************** 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: 17 poor density : 80 time to evaluate : 0.231 Fit side-chains REVERT: A 425 ASP cc_start: 0.8032 (t0) cc_final: 0.7635 (t0) REVERT: A 447 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: A 498 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: A 503 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7203 (mt-10) REVERT: A 593 LYS cc_start: 0.8081 (mttm) cc_final: 0.7615 (mttp) REVERT: A 595 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: A 673 MET cc_start: 0.8448 (ptp) cc_final: 0.7952 (ptp) REVERT: A 679 LYS cc_start: 0.7650 (tttt) cc_final: 0.6641 (tttt) REVERT: A 724 MET cc_start: 0.8640 (tmm) cc_final: 0.8420 (ttp) REVERT: A 787 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7258 (mp0) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.5988 time to fit residues: 57.6444 Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 36 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 451 GLN A 457 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108324 restraints weight = 6229.999| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.75 r_work: 0.3015 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6236 Z= 0.101 Angle : 0.503 9.231 8537 Z= 0.237 Chirality : 0.039 0.179 970 Planarity : 0.003 0.036 997 Dihedral : 13.942 89.659 1143 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.45 % Allowed : 15.13 % Favored : 81.41 % 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: -0.09 (0.32), residues: 680 helix: 2.22 (0.30), residues: 310 sheet: -2.13 (0.45), residues: 110 loop : -2.00 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 859 TYR 0.015 0.001 TYR A 566 PHE 0.015 0.001 PHE A 853 TRP 0.003 0.001 TRP A 512 HIS 0.001 0.000 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6233) covalent geometry : angle 0.50341 ( 8537) hydrogen bonds : bond 0.03320 ( 285) hydrogen bonds : angle 3.39573 ( 803) metal coordination : bond 0.00219 ( 3) *********************** 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 92 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.151 Fit side-chains REVERT: A 340 ASN cc_start: 0.8676 (m-40) cc_final: 0.8453 (m110) REVERT: A 425 ASP cc_start: 0.8270 (t0) cc_final: 0.7844 (t0) REVERT: A 498 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: A 503 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7234 (mt-10) REVERT: A 593 LYS cc_start: 0.8197 (mttm) cc_final: 0.7721 (mttp) REVERT: A 653 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8123 (pp) REVERT: A 673 MET cc_start: 0.8501 (ptp) cc_final: 0.8047 (ptp) REVERT: A 679 LYS cc_start: 0.7613 (tttt) cc_final: 0.6616 (tttm) REVERT: A 730 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7345 (ttm-80) outliers start: 21 outliers final: 8 residues processed: 87 average time/residue: 0.6020 time to fit residues: 54.6583 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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 653 LEU Chi-restraints excluded: chain A residue 730 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 451 GLN A 457 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108447 restraints weight = 6286.578| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.77 r_work: 0.2913 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6236 Z= 0.092 Angle : 0.492 8.410 8537 Z= 0.232 Chirality : 0.038 0.151 970 Planarity : 0.003 0.035 997 Dihedral : 13.862 91.127 1143 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.62 % Allowed : 16.28 % Favored : 80.10 % 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: 0.23 (0.33), residues: 680 helix: 2.47 (0.30), residues: 309 sheet: -2.07 (0.44), residues: 112 loop : -1.73 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.014 0.001 TYR A 566 PHE 0.015 0.001 PHE A 853 TRP 0.003 0.001 TRP A 908 HIS 0.005 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6233) covalent geometry : angle 0.49235 ( 8537) hydrogen bonds : bond 0.03116 ( 285) hydrogen bonds : angle 3.32050 ( 803) metal coordination : bond 0.00117 ( 3) *********************** 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 93 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.239 Fit side-chains REVERT: A 411 SER cc_start: 0.8848 (p) cc_final: 0.8563 (t) REVERT: A 425 ASP cc_start: 0.8232 (t0) cc_final: 0.7799 (t0) REVERT: A 470 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8166 (mttm) REVERT: A 479 MET cc_start: 0.8763 (ttm) cc_final: 0.8513 (mtm) REVERT: A 498 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 503 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7240 (mt-10) REVERT: A 593 LYS cc_start: 0.8195 (mttm) cc_final: 0.7436 (mttp) REVERT: A 653 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8136 (pp) REVERT: A 673 MET cc_start: 0.8449 (ptp) cc_final: 0.7983 (ptp) REVERT: A 679 LYS cc_start: 0.7632 (tttt) cc_final: 0.6624 (tttm) REVERT: A 859 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8360 (mmt90) REVERT: A 882 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6924 (p90) outliers start: 22 outliers final: 11 residues processed: 86 average time/residue: 0.5633 time to fit residues: 50.6982 Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 653 LEU Chi-restraints excluded: chain A residue 721 VAL 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 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 451 GLN A 457 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.126228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.098307 restraints weight = 6366.790| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.82 r_work: 0.2786 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6236 Z= 0.194 Angle : 0.597 10.246 8537 Z= 0.293 Chirality : 0.043 0.149 970 Planarity : 0.004 0.034 997 Dihedral : 14.093 101.019 1143 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.28 % Allowed : 16.28 % Favored : 79.44 % 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: 0.10 (0.33), residues: 680 helix: 2.16 (0.29), residues: 315 sheet: -1.98 (0.44), residues: 110 loop : -1.70 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.015 0.002 TYR A 566 PHE 0.026 0.002 PHE A 853 TRP 0.008 0.002 TRP A 771 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6233) covalent geometry : angle 0.59695 ( 8537) hydrogen bonds : bond 0.04281 ( 285) hydrogen bonds : angle 3.61318 ( 803) metal coordination : bond 0.00248 ( 3) *********************** 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 90 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 470 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8202 (mttm) REVERT: A 479 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8650 (mtm) REVERT: A 498 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: A 503 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7584 (mt-10) REVERT: A 569 ASP cc_start: 0.8374 (t0) cc_final: 0.8168 (t0) REVERT: A 591 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 593 LYS cc_start: 0.8263 (mttm) cc_final: 0.7536 (mttp) REVERT: A 595 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: A 613 ASP cc_start: 0.8197 (t0) cc_final: 0.7926 (t0) REVERT: A 653 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8013 (pp) REVERT: A 679 LYS cc_start: 0.7890 (tttt) cc_final: 0.6950 (tttm) REVERT: A 730 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7817 (ttm-80) REVERT: A 787 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 882 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6827 (p90) outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.6510 time to fit residues: 56.4659 Evaluate side-chains 79 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 MET 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 721 VAL Chi-restraints excluded: chain A residue 730 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109624 restraints weight = 6171.725| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.78 r_work: 0.2847 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2532 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= 0.097 Angle : 0.507 8.544 8537 Z= 0.244 Chirality : 0.038 0.147 970 Planarity : 0.003 0.036 997 Dihedral : 13.961 100.266 1143 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.95 % Allowed : 17.60 % 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 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: 0.37 (0.33), residues: 680 helix: 2.44 (0.30), residues: 315 sheet: -2.01 (0.43), residues: 110 loop : -1.56 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 859 TYR 0.014 0.001 TYR A 566 PHE 0.017 0.001 PHE A 853 TRP 0.004 0.001 TRP A 908 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6233) covalent geometry : angle 0.50704 ( 8537) hydrogen bonds : bond 0.03183 ( 285) hydrogen bonds : angle 3.36994 ( 803) metal coordination : bond 0.00130 ( 3) *********************** 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 89 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.237 Fit side-chains REVERT: A 425 ASP cc_start: 0.8039 (t0) cc_final: 0.7594 (t0) REVERT: A 479 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8464 (mtm) REVERT: A 498 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: A 503 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7370 (mt-10) REVERT: A 591 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: A 593 LYS cc_start: 0.7992 (mttm) cc_final: 0.7259 (mttp) REVERT: A 595 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 653 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7981 (pp) REVERT: A 679 LYS cc_start: 0.7575 (tttt) cc_final: 0.6569 (tttm) REVERT: A 730 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7018 (ttm-80) REVERT: A 767 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7532 (ttp-110) REVERT: A 882 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6854 (p90) outliers start: 24 outliers final: 10 residues processed: 82 average time/residue: 0.6990 time to fit residues: 59.7579 Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 GLU 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 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 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.124967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096664 restraints weight = 6303.598| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.85 r_work: 0.2758 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6236 Z= 0.193 Angle : 0.594 10.257 8537 Z= 0.291 Chirality : 0.043 0.173 970 Planarity : 0.004 0.035 997 Dihedral : 14.119 109.280 1143 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.29 % Allowed : 17.60 % Favored : 79.11 % 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: 0.22 (0.33), residues: 680 helix: 2.20 (0.29), residues: 316 sheet: -2.13 (0.43), residues: 114 loop : -1.44 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 664 TYR 0.014 0.002 TYR A 566 PHE 0.026 0.002 PHE A 853 TRP 0.005 0.001 TRP A 908 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 6233) covalent geometry : angle 0.59363 ( 8537) hydrogen bonds : bond 0.04194 ( 285) hydrogen bonds : angle 3.56445 ( 803) metal coordination : bond 0.00220 ( 3) *********************** 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 82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.245 Fit side-chains REVERT: A 479 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (mtm) REVERT: A 498 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: A 503 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7586 (mt-10) REVERT: A 591 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: A 593 LYS cc_start: 0.8268 (mttm) cc_final: 0.7962 (mtpp) REVERT: A 595 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 613 ASP cc_start: 0.8206 (t0) cc_final: 0.7933 (t0) REVERT: A 653 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 679 LYS cc_start: 0.7898 (tttt) cc_final: 0.6954 (tttm) REVERT: A 730 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7897 (ttm-80) REVERT: A 778 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7180 (tp30) REVERT: A 882 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6893 (p90) outliers start: 20 outliers final: 11 residues processed: 76 average time/residue: 0.6853 time to fit residues: 54.2798 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 : 0.235 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 GLU 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 728 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.134151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107474 restraints weight = 6253.802| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.69 r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2702 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= 0.102 Angle : 0.523 8.656 8537 Z= 0.253 Chirality : 0.039 0.140 970 Planarity : 0.003 0.036 997 Dihedral : 13.988 108.909 1143 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.45 % Allowed : 17.76 % Favored : 78.78 % 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: 0.40 (0.33), residues: 680 helix: 2.42 (0.29), residues: 315 sheet: -2.14 (0.42), residues: 114 loop : -1.40 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 664 TYR 0.014 0.001 TYR A 566 PHE 0.018 0.001 PHE A 853 TRP 0.005 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6233) covalent geometry : angle 0.52312 ( 8537) hydrogen bonds : bond 0.03275 ( 285) hydrogen bonds : angle 3.39715 ( 803) metal coordination : bond 0.00100 ( 3) *********************** 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 82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.236 Fit side-chains REVERT: A 479 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8589 (mtm) REVERT: A 498 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: A 503 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7554 (mt-10) REVERT: A 591 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: A 593 LYS cc_start: 0.8263 (mttm) cc_final: 0.7543 (mttp) REVERT: A 595 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: A 653 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 679 LYS cc_start: 0.7862 (tttt) cc_final: 0.6915 (tttm) REVERT: A 730 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7293 (ttm-80) REVERT: A 767 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7721 (ttp-110) REVERT: A 882 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7011 (p90) outliers start: 21 outliers final: 11 residues processed: 76 average time/residue: 0.6859 time to fit residues: 54.4232 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 GLU 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 853 PHE 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 17 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3310 r_free = 0.3310 target = 0.125971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097509 restraints weight = 6333.620| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.88 r_work: 0.2759 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6236 Z= 0.188 Angle : 0.589 10.190 8537 Z= 0.287 Chirality : 0.042 0.165 970 Planarity : 0.004 0.035 997 Dihedral : 14.123 116.711 1143 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % 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 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: 0.32 (0.33), residues: 680 helix: 2.27 (0.29), residues: 316 sheet: -2.11 (0.43), residues: 114 loop : -1.35 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 664 TYR 0.014 0.002 TYR A 566 PHE 0.026 0.002 PHE A 853 TRP 0.005 0.001 TRP A 908 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6233) covalent geometry : angle 0.58892 ( 8537) hydrogen bonds : bond 0.04105 ( 285) hydrogen bonds : angle 3.54172 ( 803) metal coordination : bond 0.00213 ( 3) *********************** 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 87 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.236 Fit side-chains REVERT: A 479 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: A 498 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 503 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7561 (mt-10) REVERT: A 542 THR cc_start: 0.8845 (p) cc_final: 0.8621 (p) REVERT: A 591 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: A 593 LYS cc_start: 0.8252 (mttm) cc_final: 0.7904 (mtpp) REVERT: A 595 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: A 613 ASP cc_start: 0.8218 (t0) cc_final: 0.7944 (t0) REVERT: A 653 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 679 LYS cc_start: 0.7796 (tttt) cc_final: 0.6832 (tttm) REVERT: A 730 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7657 (ttm-80) REVERT: A 778 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7071 (tp30) REVERT: A 882 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6962 (p90) outliers start: 25 outliers final: 12 residues processed: 81 average time/residue: 0.6809 time to fit residues: 57.6334 Evaluate side-chains 82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 GLU 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 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 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.131010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103060 restraints weight = 6259.829| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.87 r_work: 0.2905 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6236 Z= 0.113 Angle : 0.538 9.002 8537 Z= 0.260 Chirality : 0.039 0.140 970 Planarity : 0.003 0.036 997 Dihedral : 14.020 116.810 1143 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.45 % Allowed : 18.42 % Favored : 78.12 % 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: 0.44 (0.33), residues: 680 helix: 2.45 (0.29), residues: 315 sheet: -2.10 (0.43), residues: 114 loop : -1.36 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 859 TYR 0.015 0.001 TYR A 566 PHE 0.020 0.001 PHE A 853 TRP 0.005 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6233) covalent geometry : angle 0.53831 ( 8537) hydrogen bonds : bond 0.03398 ( 285) hydrogen bonds : angle 3.42798 ( 803) metal coordination : bond 0.00090 ( 3) ********************** 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 85 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.223 Fit side-chains REVERT: A 425 ASP cc_start: 0.8153 (t0) cc_final: 0.7714 (t0) REVERT: A 479 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8617 (mtm) REVERT: A 498 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: A 503 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7457 (mt-10) REVERT: A 591 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: A 593 LYS cc_start: 0.8237 (mttm) cc_final: 0.7498 (mttp) REVERT: A 595 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: A 613 ASP cc_start: 0.8053 (t0) cc_final: 0.7721 (t70) REVERT: A 653 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 679 LYS cc_start: 0.7814 (tttt) cc_final: 0.6854 (tttm) REVERT: A 730 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7150 (ttm-80) REVERT: A 767 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7683 (ttp-110) REVERT: A 882 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6957 (p90) outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 0.7228 time to fit residues: 60.2951 Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 GLU 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 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 25 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100631 restraints weight = 6284.897| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.84 r_work: 0.3008 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2782 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= 0.111 Angle : 0.539 11.102 8537 Z= 0.257 Chirality : 0.039 0.154 970 Planarity : 0.003 0.037 997 Dihedral : 13.967 118.661 1143 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.12 % Allowed : 18.42 % 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 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 (0.33), residues: 680 helix: 2.50 (0.29), residues: 315 sheet: -2.04 (0.43), residues: 114 loop : -1.34 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 859 TYR 0.014 0.001 TYR A 566 PHE 0.019 0.001 PHE A 853 TRP 0.005 0.001 TRP A 908 HIS 0.002 0.000 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6233) covalent geometry : angle 0.53867 ( 8537) hydrogen bonds : bond 0.03311 ( 285) hydrogen bonds : angle 3.36830 ( 803) metal coordination : bond 0.00107 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.77 seconds wall clock time: 36 minutes 31.81 seconds (2191.81 seconds total)