Starting phenix.real_space_refine on Thu Jul 2 02:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e28_27828/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2026/8e28_27828.map" } 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-dev-6108/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: {'RNA': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 8} Time building chain proxies: 1.09, per 1000 atoms: 0.19 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: 0.47 Conformation dependent library (CDL) restraints added in 223.2 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: 0.47 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: 0.95 Time building geometry restraints manager: 0.65 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: 7829 2.06 - 4.13: 221 4.13 - 6.19: 36 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: 3040 16.13 - 32.25: 423 32.25 - 48.38: 123 48.38 - 64.51: 24 64.51 - 80.63: 11 Dihedral angle restraints: 3621 sinusoidal: 1597 harmonic: 2024 Sorted by residual: dihedral pdb=" CA PHE A 464 " pdb=" C PHE A 464 " pdb=" N SER A 465 " pdb=" CA SER A 465 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 633 0.043 - 0.086: 212 0.086 - 0.129: 65 0.129 - 0.172: 16 0.172 - 0.215: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CB ILE A 856 " pdb=" CA ILE A 856 " pdb=" CG1 ILE A 856 " pdb=" CG2 ILE A 856 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (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: 2.210 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: 0.010 Set scattering table: 0.010 Process input model: 7.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- 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= 0.193 Angle : 0.832 10.320 8097 Z= 0.443 Chirality : 0.049 0.215 928 Planarity : 0.007 0.062 997 Dihedral : 16.454 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 0.00395 / 0.19 ( 5937) covalent geometry : angle 0.83152 / 0.44 ( 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 : 0.222 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: 0.0616 time to fit residues: 5.1963 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 : 0.208 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.131271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103664 restraints weight = 7102.337| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.83 r_work: 0.3032 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5937 Z= 0.219 Angle : 0.609 6.650 8097 Z= 0.314 Chirality : 0.045 0.159 928 Planarity : 0.006 0.058 997 Dihedral : 7.971 71.600 924 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.82 % Allowed : 9.39 % Favored : 89.79 % 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: -0.04 (0.43), residues: 156 loop : -1.62 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 231 TYR 0.013 0.002 TYR A 674 PHE 0.020 0.002 PHE A 464 TRP 0.021 0.002 TRP A 468 HIS 0.004 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 ( 5937) covalent geometry : angle 0.60894 / 0.31 ( 8097) hydrogen bonds : bond 0.06394 / 4.32 ( 216) hydrogen bonds : angle 4.70575 / 3.20 ( 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 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.211 Fit side-chains REVERT: A 51 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7236 (pt0) REVERT: A 334 GLU cc_start: 0.8420 (tt0) cc_final: 0.8098 (tt0) REVERT: A 628 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.5762 (mtt) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.0891 time to fit residues: 6.4243 Evaluate side-chains 54 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 804 SER 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: 0.7980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102825 restraints weight = 7069.019| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.91 r_work: 0.3040 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.132 Angle : 0.513 5.356 8097 Z= 0.264 Chirality : 0.042 0.143 928 Planarity : 0.005 0.043 997 Dihedral : 7.773 70.735 924 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.65 % Allowed : 12.69 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.31), residues: 684 helix: 0.49 (0.37), residues: 204 sheet: 0.17 (0.44), residues: 153 loop : -1.38 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.010 0.001 TYR A 340 PHE 0.011 0.002 PHE A 481 TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 5937) covalent geometry : angle 0.51330 / 0.26 ( 8097) hydrogen bonds : bond 0.05144 / 3.49 ( 216) hydrogen bonds : angle 4.43297 / 3.01 ( 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 66 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.215 Fit side-chains REVERT: A 51 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7088 (pt0) REVERT: A 334 GLU cc_start: 0.8407 (tt0) cc_final: 0.8016 (tt0) REVERT: A 737 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: A 764 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6037 (mp0) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.1013 time to fit residues: 7.5980 Evaluate side-chains 58 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102132 restraints weight = 7114.065| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.91 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5937 Z= 0.143 Angle : 0.511 5.213 8097 Z= 0.262 Chirality : 0.042 0.139 928 Planarity : 0.005 0.039 997 Dihedral : 7.690 70.511 924 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.81 % Allowed : 15.98 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.32), residues: 684 helix: 0.69 (0.37), residues: 204 sheet: 0.48 (0.43), residues: 156 loop : -1.33 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 231 TYR 0.010 0.001 TYR A 340 PHE 0.012 0.001 PHE A 481 TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 5937) covalent geometry : angle 0.51097 / 0.26 ( 8097) hydrogen bonds : bond 0.05206 / 3.54 ( 216) hydrogen bonds : angle 4.35594 / 2.96 ( 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 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.225 Fit side-chains REVERT: A 51 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7068 (pt0) REVERT: A 334 GLU cc_start: 0.8473 (tt0) cc_final: 0.8032 (tt0) REVERT: A 628 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5625 (mtt) REVERT: A 737 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 764 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6050 (mp0) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.0899 time to fit residues: 6.6131 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.131887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103006 restraints weight = 7226.346| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.94 r_work: 0.3042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1553 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= 0.120 Angle : 0.487 5.298 8097 Z= 0.250 Chirality : 0.041 0.136 928 Planarity : 0.004 0.036 997 Dihedral : 7.613 70.467 924 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.22 % 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: -0.23 (0.32), residues: 684 helix: 0.88 (0.37), residues: 204 sheet: 0.56 (0.44), residues: 156 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 0.002 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 5937) covalent geometry : angle 0.48658 / 0.25 ( 8097) hydrogen bonds : bond 0.04788 / 3.26 ( 216) hydrogen bonds : angle 4.25713 / 2.88 ( 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 66 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.207 Fit side-chains REVERT: A 51 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7064 (pt0) REVERT: A 334 GLU cc_start: 0.8449 (tt0) cc_final: 0.7976 (tt0) REVERT: A 352 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 628 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5635 (mtt) REVERT: A 737 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: A 764 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6034 (mp0) outliers start: 14 outliers final: 8 residues processed: 59 average time/residue: 0.0834 time to fit residues: 6.4367 Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105379 restraints weight = 7146.498| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.92 r_work: 0.3076 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1579 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= 0.092 Angle : 0.455 5.286 8097 Z= 0.233 Chirality : 0.040 0.132 928 Planarity : 0.004 0.032 997 Dihedral : 7.494 70.440 924 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.81 % Allowed : 17.30 % Favored : 80.89 % 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: 1.12 (0.37), residues: 204 sheet: 0.70 (0.43), residues: 156 loop : -1.07 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 5937) covalent geometry : angle 0.45517 / 0.23 ( 8097) hydrogen bonds : bond 0.04065 / 2.77 ( 216) hydrogen bonds : angle 4.09162 / 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 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.202 Fit side-chains REVERT: A 51 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7024 (pt0) REVERT: A 334 GLU cc_start: 0.8441 (tt0) cc_final: 0.8048 (tt0) REVERT: A 352 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 764 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5821 (mp0) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.0747 time to fit residues: 5.6396 Evaluate side-chains 58 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.128994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099949 restraints weight = 7261.832| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.94 r_work: 0.2928 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1787 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= 0.225 Angle : 0.572 5.730 8097 Z= 0.291 Chirality : 0.044 0.146 928 Planarity : 0.005 0.040 997 Dihedral : 7.673 70.610 924 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 17.79 % Favored : 79.74 % 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: -0.36 (0.32), residues: 684 helix: 0.70 (0.37), residues: 204 sheet: 0.35 (0.44), residues: 160 loop : -1.16 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.012 0.002 TYR A 653 PHE 0.019 0.002 PHE A 481 TRP 0.013 0.002 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 ( 5937) covalent geometry : angle 0.57192 / 0.29 ( 8097) hydrogen bonds : bond 0.06155 / 4.18 ( 216) hydrogen bonds : angle 4.42240 / 3.01 ( 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 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.224 Fit side-chains REVERT: A 51 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7080 (pt0) REVERT: A 334 GLU cc_start: 0.8540 (tt0) cc_final: 0.8125 (tt0) REVERT: A 352 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 657 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7601 (mmt90) REVERT: A 737 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: A 764 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6221 (mp0) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 0.0820 time to fit residues: 6.1307 Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 10.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.133236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104687 restraints weight = 7109.210| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.91 r_work: 0.3060 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1691 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= 0.096 Angle : 0.466 5.243 8097 Z= 0.240 Chirality : 0.040 0.133 928 Planarity : 0.004 0.033 997 Dihedral : 7.497 70.162 924 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.14 % Allowed : 18.45 % Favored : 79.41 % 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 are not related in a simple way. whole: 0.01 (0.33), residues: 684 helix: 1.11 (0.37), residues: 205 sheet: 0.66 (0.43), residues: 157 loop : -1.06 (0.34), residues: 322 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 0.017 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 5937) covalent geometry : angle 0.46568 / 0.24 ( 8097) hydrogen bonds : bond 0.04293 / 2.93 ( 216) hydrogen bonds : angle 4.14152 / 2.81 ( 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 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.148 Fit side-chains REVERT: A 51 GLU cc_start: 0.8013 (mm-30) cc_final: 0.6946 (pt0) REVERT: A 334 GLU cc_start: 0.8398 (tt0) cc_final: 0.7972 (tt0) REVERT: A 352 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 657 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7431 (mmt90) REVERT: A 764 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.5893 (mp0) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.0852 time to fit residues: 6.2934 Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 18 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.136461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108598 restraints weight = 7174.664| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.86 r_work: 0.3066 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5937 Z= 0.083 Angle : 0.441 5.236 8097 Z= 0.225 Chirality : 0.040 0.137 928 Planarity : 0.004 0.033 997 Dihedral : 7.363 70.004 924 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.81 % Allowed : 18.95 % 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: 0.09 (0.33), residues: 684 helix: 1.22 (0.38), residues: 210 sheet: 0.64 (0.43), residues: 154 loop : -1.03 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.008 0.001 TYR A 674 PHE 0.012 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 ( 5937) covalent geometry : angle 0.44108 / 0.23 ( 8097) hydrogen bonds : bond 0.03611 / 2.46 ( 216) hydrogen bonds : angle 3.98042 / 2.68 ( 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: 11 poor density : 48 time to evaluate : 0.140 Fit side-chains REVERT: A 51 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7036 (pt0) REVERT: A 334 GLU cc_start: 0.8446 (tt0) cc_final: 0.8032 (tt0) REVERT: A 352 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 657 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7326 (mmt90) REVERT: A 764 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5710 (mp0) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.0656 time to fit residues: 5.0687 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.135547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107038 restraints weight = 7233.376| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.94 r_work: 0.3032 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1735 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= 0.088 Angle : 0.446 5.122 8097 Z= 0.227 Chirality : 0.040 0.135 928 Planarity : 0.004 0.032 997 Dihedral : 7.265 69.782 924 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.81 % Allowed : 19.28 % Favored : 78.91 % 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: 0.16 (0.33), residues: 684 helix: 1.23 (0.37), residues: 211 sheet: 0.67 (0.43), residues: 154 loop : -0.95 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.007 0.001 TYR A 653 PHE 0.011 0.001 PHE A 648 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 5937) covalent geometry : angle 0.44580 / 0.23 ( 8097) hydrogen bonds : bond 0.03829 / 2.62 ( 216) hydrogen bonds : angle 3.98916 / 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 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.167 Fit side-chains REVERT: A 51 GLU cc_start: 0.7988 (mm-30) cc_final: 0.6971 (pt0) REVERT: A 334 GLU cc_start: 0.8464 (tt0) cc_final: 0.8055 (tt0) REVERT: A 352 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 657 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7443 (mmt90) REVERT: A 764 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5814 (mp0) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.0775 time to fit residues: 5.9189 Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU 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 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.136170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107908 restraints weight = 7107.402| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.91 r_work: 0.3114 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5937 Z= 0.083 Angle : 0.440 5.164 8097 Z= 0.224 Chirality : 0.039 0.133 928 Planarity : 0.004 0.031 997 Dihedral : 7.199 69.635 924 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 19.28 % Favored : 78.91 % 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 (0.33), residues: 684 helix: 1.29 (0.37), residues: 211 sheet: 0.67 (0.43), residues: 154 loop : -0.92 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.007 0.001 TYR A 653 PHE 0.012 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.08 ( 5937) covalent geometry : angle 0.44005 / 0.22 ( 8097) hydrogen bonds : bond 0.03675 / 2.51 ( 216) hydrogen bonds : angle 3.95481 / 2.66 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1398.63 seconds wall clock time: 24 minutes 37.57 seconds (1477.57 seconds total)