Starting phenix.real_space_refine on Tue Aug 4 18:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e28_27828/08_2026/8e28_27828.cif" } resolution = 3.1 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= 0.003 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 31 5.16 5 C 3638 2.51 5 N 976 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5789 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5489 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 41, 'TRANS': 648} Chain breaks: 2 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'RNAv2': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 8} Time building chain proxies: 1.43, per 1000 atoms: 0.25 Number of scatterers: 5789 At special positions: 0 Unit cell: (79.86, 86.46, 93.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 15 15.00 O 1129 8.00 N 976 7.00 C 3638 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: 0.44 Conformation dependent library (CDL) restraints added in 317.3 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 10 sheets defined 32.0% alpha, 23.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.438A pdb=" N ASP A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.889A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.765A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.771A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.846A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.598A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.674A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.636A pdb=" N GLN A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 764 removed outlier: 3.557A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.253A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.783A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.424A pdb=" N ARG A 487 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.481A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.430A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.715A pdb=" N GLY A 776 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 785 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 774 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 802 through 809 removed outlier: 6.713A pdb=" N VAL A 819 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A 805 " --> pdb=" O THR A 817 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 817 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 807 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 815 " --> pdb=" O PHE A 807 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.60 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: 1626 1.34 - 1.45: 952 1.45 - 1.57: 3283 1.57 - 1.69: 29 1.69 - 1.81: 47 Bond restraints: 5937 Sorted by residual: bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" C GLU A 330 " pdb=" N PRO A 331 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.76e+00 bond pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 7775 2.06 - 4.13: 264 4.13 - 6.19: 47 6.19 - 8.26: 7 8.26 - 10.32: 4 Bond angle restraints: 8097 Sorted by residual: angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 120.35 -8.35 2.20e+00 2.07e-01 1.44e+01 angle pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 112.60 118.96 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" N ASN A 391 " pdb=" CA ASN A 391 " pdb=" C ASN A 391 " ideal model delta sigma weight residual 113.17 117.74 -4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" CA LYS A 283 " pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 111.37 115.62 -4.25 1.29e+00 6.01e-01 1.09e+01 ... (remaining 8092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 2989 16.13 - 32.25: 446 32.25 - 48.38: 129 48.38 - 64.51: 41 64.51 - 80.63: 16 Dihedral angle restraints: 3621 sinusoidal: 1597 harmonic: 2024 Sorted by residual: dihedral pdb=" C4' U C 3 " pdb=" C3' U C 3 " pdb=" C2' U C 3 " pdb=" C1' U C 3 " ideal model delta sinusoidal sigma weight residual 36.34 -35.78 72.13 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' U C 6 " pdb=" C3' U C 6 " pdb=" C2' U C 6 " pdb=" C1' U C 6 " ideal model delta sinusoidal sigma weight residual 36.35 -35.67 72.01 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" C2' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual 36.34 -34.97 71.32 1 3.10e+00 1.04e-01 6.79e+02 ... (remaining 3618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 716 0.056 - 0.113: 149 0.113 - 0.169: 34 0.169 - 0.225: 8 0.225 - 0.282: 21 Chirality restraints: 928 Sorted by residual: chirality pdb=" C2' C C 1 " pdb=" C3' C C 1 " pdb=" O2' C C 1 " pdb=" C1' C C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' U C 2 " pdb=" C3' U C 2 " pdb=" O2' U C 2 " pdb=" C1' U C 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U C 8 " pdb=" C3' U C 8 " pdb=" O2' U C 8 " pdb=" C1' U C 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 925 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 444 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 445 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 97 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" CG ASP A 97 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 97 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 728 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 729 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.033 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1725 2.83 - 3.35: 4525 3.35 - 3.87: 8908 3.87 - 4.38: 10327 4.38 - 4.90: 18495 Nonbonded interactions: 43980 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 696 " pdb=" OP1 U C 13 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASP A 288 " pdb=" OH TYR A 296 " model vdw 2.348 3.040 nonbonded pdb=" NH2 ARG A 543 " pdb=" OE2 GLU A 584 " model vdw 2.374 3.120 nonbonded pdb=" NE2 GLN A 827 " pdb=" O GLU A 828 " model vdw 2.379 3.120 ... (remaining 43975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.660 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.004 0.048 5937 Z= 0.196 Angle : 0.883 10.320 8097 Z= 0.452 Chirality : 0.064 0.282 928 Planarity : 0.007 0.062 997 Dihedral : 17.789 80.633 2303 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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 are not related in a simple way. whole: -1.72 (0.30), residues: 684 helix: -1.10 (0.32), residues: 210 sheet: -0.21 (0.42), residues: 163 loop : -1.62 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 231 TYR 0.037 0.002 TYR A 689 PHE 0.039 0.003 PHE A 80 TRP 0.017 0.002 TRP A 468 HIS 0.010 0.002 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 ( 5937) covalent geometry : angle 0.88253 / 0.45 ( 8097) hydrogen bonds : bond 0.12497 / 7.63 ( 216) hydrogen bonds : angle 5.71008 / 3.92 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.212 Fit side-chains REVERT: A 51 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7058 (pt0) REVERT: A 495 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 586 MET cc_start: 0.8192 (mmt) cc_final: 0.7863 (mmt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0717 time to fit residues: 5.9534 Evaluate side-chains 49 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104817 restraints weight = 7089.072| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.80 r_work: 0.2966 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5937 Z= 0.230 Angle : 0.915 20.277 8097 Z= 0.386 Chirality : 0.089 0.995 928 Planarity : 0.006 0.055 997 Dihedral : 9.922 89.211 924 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.15 % Allowed : 8.73 % Favored : 90.12 % 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 are not related in a simple way. whole: -1.18 (0.30), residues: 684 helix: -0.07 (0.36), residues: 204 sheet: -0.06 (0.43), residues: 156 loop : -1.61 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.013 0.002 TYR A 674 PHE 0.021 0.002 PHE A 464 TRP 0.020 0.002 TRP A 468 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 ( 5937) covalent geometry : angle 0.91466 / 0.39 ( 8097) hydrogen bonds : bond 0.06274 / 4.24 ( 216) hydrogen bonds : angle 4.71384 / 3.21 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.133 Fit side-chains REVERT: A 51 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7189 (pt0) REVERT: A 628 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5808 (mtt) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.0606 time to fit residues: 4.4441 Evaluate side-chains 56 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102987 restraints weight = 7089.223| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.82 r_work: 0.3040 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5937 Z= 0.191 Angle : 0.713 15.899 8097 Z= 0.322 Chirality : 0.063 0.679 928 Planarity : 0.005 0.050 997 Dihedral : 10.262 115.898 924 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 13.51 % Favored : 84.35 % 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 are not related in a simple way. whole: -0.85 (0.31), residues: 684 helix: 0.29 (0.37), residues: 204 sheet: 0.20 (0.44), residues: 151 loop : -1.48 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.012 0.002 TYR A 340 PHE 0.014 0.002 PHE A 481 TRP 0.018 0.002 TRP A 468 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 5937) covalent geometry : angle 0.71305 / 0.32 ( 8097) hydrogen bonds : bond 0.05928 / 4.02 ( 216) hydrogen bonds : angle 4.54285 / 3.09 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.218 Fit side-chains REVERT: A 51 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7199 (pt0) REVERT: A 334 GLU cc_start: 0.8369 (tt0) cc_final: 0.8137 (tt0) REVERT: A 737 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 764 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6176 (mp0) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.1095 time to fit residues: 8.4933 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103345 restraints weight = 7138.227| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.87 r_work: 0.3091 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.103 Angle : 0.609 12.238 8097 Z= 0.274 Chirality : 0.053 0.442 928 Planarity : 0.004 0.033 997 Dihedral : 10.169 116.811 924 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.32 % Allowed : 16.31 % Favored : 82.37 % 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 are not related in a simple way. whole: -0.30 (0.32), residues: 684 helix: 0.82 (0.38), residues: 204 sheet: 0.52 (0.44), residues: 156 loop : -1.24 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 231 TYR 0.009 0.001 TYR A 340 PHE 0.009 0.001 PHE A 782 TRP 0.015 0.001 TRP A 468 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 5937) covalent geometry : angle 0.60867 / 0.27 ( 8097) hydrogen bonds : bond 0.04304 / 2.93 ( 216) hydrogen bonds : angle 4.22234 / 2.85 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.136 Fit side-chains REVERT: A 51 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7076 (pt0) REVERT: A 334 GLU cc_start: 0.8398 (tt0) cc_final: 0.8144 (tt0) REVERT: A 628 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5600 (mtt) REVERT: A 764 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.5816 (mp0) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.0892 time to fit residues: 6.4965 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.103870 restraints weight = 7224.090| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.93 r_work: 0.2971 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5937 Z= 0.128 Angle : 0.615 12.153 8097 Z= 0.278 Chirality : 0.053 0.426 928 Planarity : 0.004 0.034 997 Dihedral : 10.127 118.146 924 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.81 % Allowed : 17.46 % Favored : 80.72 % 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 are not related in a simple way. whole: -0.18 (0.32), residues: 684 helix: 0.90 (0.37), residues: 204 sheet: 0.60 (0.44), residues: 156 loop : -1.16 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 231 TYR 0.009 0.001 TYR A 340 PHE 0.013 0.001 PHE A 481 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 5937) covalent geometry : angle 0.61474 / 0.28 ( 8097) hydrogen bonds : bond 0.04784 / 3.26 ( 216) hydrogen bonds : angle 4.21441 / 2.85 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.226 Fit side-chains REVERT: A 51 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7050 (pt0) REVERT: A 334 GLU cc_start: 0.8470 (tt0) cc_final: 0.8102 (tt0) REVERT: A 352 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 628 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5674 (mtt) REVERT: A 764 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6046 (mp0) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.1012 time to fit residues: 7.7099 Evaluate side-chains 58 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104506 restraints weight = 7185.384| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.87 r_work: 0.3095 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.098 Angle : 0.572 9.920 8097 Z= 0.260 Chirality : 0.050 0.364 928 Planarity : 0.004 0.033 997 Dihedral : 10.094 118.274 924 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.81 % Allowed : 18.12 % Favored : 80.07 % 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 are not related in a simple way. whole: -0.01 (0.33), residues: 684 helix: 1.09 (0.38), residues: 204 sheet: 0.65 (0.43), residues: 156 loop : -1.07 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.010 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.003 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 5937) covalent geometry : angle 0.57238 / 0.26 ( 8097) hydrogen bonds : bond 0.04112 / 2.81 ( 216) hydrogen bonds : angle 4.08837 / 2.76 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.226 Fit side-chains REVERT: A 51 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7046 (pt0) REVERT: A 334 GLU cc_start: 0.8408 (tt0) cc_final: 0.8026 (tt0) REVERT: A 352 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 628 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5715 (mtt) REVERT: A 657 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7507 (mmt90) REVERT: A 764 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.5839 (mp0) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.0919 time to fit residues: 6.8855 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102155 restraints weight = 7267.757| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.94 r_work: 0.2928 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5937 Z= 0.166 Angle : 0.633 11.575 8097 Z= 0.289 Chirality : 0.053 0.443 928 Planarity : 0.004 0.035 997 Dihedral : 10.263 118.092 924 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.64 % Allowed : 18.12 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.32), residues: 684 helix: 0.90 (0.37), residues: 204 sheet: 0.34 (0.43), residues: 160 loop : -1.07 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.010 0.001 TYR A 653 PHE 0.015 0.002 PHE A 481 TRP 0.013 0.002 TRP A 468 HIS 0.002 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 5937) covalent geometry : angle 0.63305 / 0.29 ( 8097) hydrogen bonds : bond 0.05360 / 3.65 ( 216) hydrogen bonds : angle 4.26315 / 2.90 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.226 Fit side-chains REVERT: A 51 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7027 (pt0) REVERT: A 334 GLU cc_start: 0.8497 (tt0) cc_final: 0.8076 (tt0) REVERT: A 352 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 628 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5660 (mtt) REVERT: A 657 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7486 (mmt90) REVERT: A 737 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: A 764 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6124 (mp0) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.1019 time to fit residues: 7.9910 Evaluate side-chains 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106372 restraints weight = 7101.238| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.91 r_work: 0.3098 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5937 Z= 0.096 Angle : 0.559 8.699 8097 Z= 0.256 Chirality : 0.049 0.358 928 Planarity : 0.004 0.032 997 Dihedral : 10.110 117.943 924 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.47 % Allowed : 18.45 % Favored : 79.08 % 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 are not related in a simple way. whole: 0.10 (0.33), residues: 684 helix: 1.22 (0.38), residues: 204 sheet: 0.71 (0.43), residues: 154 loop : -1.02 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.011 0.001 PHE A 648 TRP 0.015 0.001 TRP A 468 HIS 0.003 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 5937) covalent geometry : angle 0.55946 / 0.26 ( 8097) hydrogen bonds : bond 0.04051 / 2.76 ( 216) hydrogen bonds : angle 4.06465 / 2.75 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.230 Fit side-chains REVERT: A 51 GLU cc_start: 0.8002 (mm-30) cc_final: 0.6918 (pt0) REVERT: A 334 GLU cc_start: 0.8368 (tt0) cc_final: 0.7942 (tt0) REVERT: A 352 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 628 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5686 (mtt) REVERT: A 657 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7440 (mmt90) REVERT: A 764 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.5751 (mp0) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 0.0975 time to fit residues: 7.3516 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106616 restraints weight = 7187.399| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.93 r_work: 0.3094 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.099 Angle : 0.553 8.733 8097 Z= 0.254 Chirality : 0.048 0.315 928 Planarity : 0.004 0.033 997 Dihedral : 9.990 119.897 924 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.98 % Allowed : 18.95 % Favored : 79.08 % 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 are not related in a simple way. whole: 0.02 (0.33), residues: 684 helix: 1.10 (0.37), residues: 211 sheet: 0.65 (0.43), residues: 156 loop : -1.07 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 231 TYR 0.008 0.001 TYR A 674 PHE 0.012 0.001 PHE A 648 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 5937) covalent geometry : angle 0.55306 / 0.25 ( 8097) hydrogen bonds : bond 0.04083 / 2.79 ( 216) hydrogen bonds : angle 4.04545 / 2.74 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.228 Fit side-chains REVERT: A 51 GLU cc_start: 0.7991 (mm-30) cc_final: 0.6923 (pt0) REVERT: A 334 GLU cc_start: 0.8398 (tt0) cc_final: 0.7959 (tt0) REVERT: A 352 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 657 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7432 (mmt90) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.0815 time to fit residues: 6.0844 Evaluate side-chains 57 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108306 restraints weight = 7242.645| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.94 r_work: 0.3124 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5937 Z= 0.089 Angle : 0.536 7.543 8097 Z= 0.247 Chirality : 0.047 0.278 928 Planarity : 0.004 0.031 997 Dihedral : 9.886 120.002 924 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.98 % Allowed : 18.95 % Favored : 79.08 % 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 are not related in a simple way. whole: 0.14 (0.33), residues: 684 helix: 1.20 (0.37), residues: 211 sheet: 0.71 (0.43), residues: 152 loop : -0.97 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.008 0.001 TYR A 674 PHE 0.011 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.003 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 5937) covalent geometry : angle 0.53573 / 0.25 ( 8097) hydrogen bonds : bond 0.03750 / 2.58 ( 216) hydrogen bonds : angle 3.98860 / 2.69 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.275 Fit side-chains REVERT: A 51 GLU cc_start: 0.7974 (mm-30) cc_final: 0.6907 (pt0) REVERT: A 334 GLU cc_start: 0.8373 (tt0) cc_final: 0.7938 (tt0) REVERT: A 352 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 657 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7402 (mmt90) REVERT: A 764 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5665 (mp0) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1076 time to fit residues: 8.3337 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102546 restraints weight = 7170.366| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.93 r_work: 0.2956 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5937 Z= 0.174 Angle : 0.625 10.682 8097 Z= 0.289 Chirality : 0.052 0.382 928 Planarity : 0.004 0.038 997 Dihedral : 9.989 120.863 924 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.98 % Allowed : 18.95 % Favored : 79.08 % 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 are not related in a simple way. whole: -0.12 (0.32), residues: 684 helix: 0.99 (0.37), residues: 205 sheet: 0.34 (0.42), residues: 161 loop : -0.99 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.011 0.002 TYR A 653 PHE 0.016 0.002 PHE A 481 TRP 0.012 0.002 TRP A 468 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 ( 5937) covalent geometry : angle 0.62507 / 0.29 ( 8097) hydrogen bonds : bond 0.05482 / 3.76 ( 216) hydrogen bonds : angle 4.27099 / 2.91 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.41 seconds wall clock time: 28 minutes 10.88 seconds (1690.88 seconds total)