Starting phenix.real_space_refine on Tue Aug 4 19:58:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6p_62131/08_2026/9k6p_62131.cif" } resolution = 3.2 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= 0.027 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 19 5.49 5 S 40 5.16 5 C 4107 2.51 5 N 1177 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 6576 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6172 Classifications: {'peptide': 772} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 726} Chain breaks: 3 Chain: "B" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Time building chain proxies: 1.32, per 1000 atoms: 0.20 Number of scatterers: 6576 At special positions: 0 Unit cell: (70.68, 91.2, 106.02, 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 40 16.00 P 19 15.00 O 1233 8.00 N 1177 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 462 " distance=2.03 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: 0.41 Conformation dependent library (CDL) restraints added in 376.1 milliseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 32.8% alpha, 15.5% beta 6 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.645A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 156 through 166 removed outlier: 4.151A pdb=" N MET A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.662A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 251 through 262 removed outlier: 4.415A pdb=" N ARG A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.183A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.510A pdb=" N PHE A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.858A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.965A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.701A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.875A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 686 " --> pdb=" O HIS A 682 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 removed outlier: 3.767A pdb=" N LYS A 720 " --> pdb=" O CYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.575A pdb=" N ILE A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 816 removed outlier: 3.841A pdb=" N TYR A 804 " --> pdb=" O PRO A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 844 Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.750A pdb=" N GLU A 46 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 400 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.234A pdb=" N ILE A 54 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N CYS A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS A 56 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 113 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.557A pdb=" N THR A 222 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.877A pdb=" N ILE A 521 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 625 through 632 removed outlier: 3.581A pdb=" N VAL A 614 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 668 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 706 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 767 " --> pdb=" O VAL A 706 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1009 1.28 - 1.41: 1756 1.41 - 1.55: 3876 1.55 - 1.69: 61 1.69 - 1.83: 60 Bond restraints: 6762 Sorted by residual: bond pdb=" CG PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 1.503 1.138 0.365 3.40e-02 8.65e+02 1.15e+02 bond pdb=" CB PRO A 527 " pdb=" CG PRO A 527 " ideal model delta sigma weight residual 1.492 1.189 0.303 5.00e-02 4.00e+02 3.68e+01 bond pdb=" CG PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CA PHE A 200 " pdb=" CB PHE A 200 " ideal model delta sigma weight residual 1.524 1.580 -0.056 1.30e-02 5.92e+03 1.84e+01 bond pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.81: 9204 7.81 - 15.61: 27 15.61 - 23.42: 1 23.42 - 31.23: 2 31.23 - 39.03: 1 Bond angle restraints: 9235 Sorted by residual: angle pdb=" N PRO A 527 " pdb=" CD PRO A 527 " pdb=" CG PRO A 527 " ideal model delta sigma weight residual 103.20 75.97 27.23 1.50e+00 4.44e-01 3.30e+02 angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 92.39 19.61 1.40e+00 5.10e-01 1.96e+02 angle pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " pdb=" CG PRO A 527 " ideal model delta sigma weight residual 104.50 78.31 26.19 1.90e+00 2.77e-01 1.90e+02 angle pdb=" CB PRO A 527 " pdb=" CG PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 106.10 145.13 -39.03 3.20e+00 9.77e-02 1.49e+02 angle pdb=" CA PRO A 762 " pdb=" N PRO A 762 " pdb=" CD PRO A 762 " ideal model delta sigma weight residual 112.00 96.79 15.21 1.40e+00 5.10e-01 1.18e+02 ... (remaining 9230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 3901 35.73 - 71.45: 217 71.45 - 107.17: 16 107.17 - 142.90: 1 142.90 - 178.62: 2 Dihedral angle restraints: 4137 sinusoidal: 1890 harmonic: 2247 Sorted by residual: dihedral pdb=" CD ARG A 812 " pdb=" NE ARG A 812 " pdb=" CZ ARG A 812 " pdb=" NH1 ARG A 812 " ideal model delta sinusoidal sigma weight residual 0.00 -82.51 82.51 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" O4' U C 18 " pdb=" C1' U C 18 " pdb=" N1 U C 18 " pdb=" C2 U C 18 " ideal model delta sinusoidal sigma weight residual -128.00 50.62 -178.62 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CD ARG A 814 " pdb=" NE ARG A 814 " pdb=" CZ ARG A 814 " pdb=" NH1 ARG A 814 " ideal model delta sinusoidal sigma weight residual 0.00 70.95 -70.95 1 1.00e+01 1.00e-02 6.47e+01 ... (remaining 4134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 900 0.099 - 0.197: 119 0.197 - 0.296: 14 0.296 - 0.395: 3 0.395 - 0.493: 5 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CB ILE A 592 " pdb=" CA ILE A 592 " pdb=" CG1 ILE A 592 " pdb=" CG2 ILE A 592 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CB ILE A 74 " pdb=" CA ILE A 74 " pdb=" CG1 ILE A 74 " pdb=" CG2 ILE A 74 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CB ILE A 651 " pdb=" CA ILE A 651 " pdb=" CG1 ILE A 651 " pdb=" CG2 ILE A 651 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 1038 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 812 " -1.096 9.50e-02 1.11e+02 4.91e-01 1.46e+02 pdb=" NE ARG A 812 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 812 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 812 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 812 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 814 " -1.044 9.50e-02 1.11e+02 4.68e-01 1.32e+02 pdb=" NE ARG A 814 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 814 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 814 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 814 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 742 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 743 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 743 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 743 " 0.061 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1335 2.78 - 3.31: 5908 3.31 - 3.84: 11859 3.84 - 4.37: 13148 4.37 - 4.90: 21993 Nonbonded interactions: 54243 Sorted by model distance: nonbonded pdb=" OH TYR A 765 " pdb=" O SER A 798 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 804 " pdb=" OP2 A B 5 " model vdw 2.292 3.040 nonbonded pdb=" O ARG A 534 " pdb=" OG1 THR A 538 " model vdw 2.299 3.040 nonbonded pdb=" O PRO A 152 " pdb=" OG1 THR A 744 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 703 " pdb=" OG1 THR A 703 " model vdw 2.302 3.040 ... (remaining 54238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 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 : 0.010 0.365 6763 Z= 0.397 Angle : 1.441 39.033 9237 Z= 0.837 Chirality : 0.074 0.493 1041 Planarity : 0.023 0.491 1121 Dihedral : 20.780 178.623 2680 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.18 % Allowed : 32.79 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -3.66 (0.25), residues: 764 helix: -2.58 (0.26), residues: 223 sheet: -2.32 (0.43), residues: 108 loop : -2.40 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 423 TYR 0.040 0.004 TYR A 749 PHE 0.030 0.003 PHE A 442 TRP 0.018 0.002 TRP A 199 HIS 0.018 0.002 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00970 / 0.40 ( 6762) covalent geometry : angle 1.44075 / 0.84 ( 9235) SS BOND : bond 0.00520 / 0.33 ( 1) SS BOND : angle 2.25442 / 0.92 ( 2) hydrogen bonds : bond 0.18260 / 11.71 ( 242) hydrogen bonds : angle 8.94774 / 6.10 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.233 Fit side-chains REVERT: A 97 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.6412 (ttp-170) REVERT: A 807 HIS cc_start: 0.4560 (OUTLIER) cc_final: 0.4303 (t70) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.1086 time to fit residues: 12.4065 Evaluate side-chains 80 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 817 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 466 HIS A 553 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.277069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.247677 restraints weight = 8895.204| |-----------------------------------------------------------------------------| r_work (start): 0.5015 rms_B_bonded: 2.55 r_work: 0.4876 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 6763 Z= 0.153 Angle : 0.749 9.649 9237 Z= 0.386 Chirality : 0.050 0.307 1041 Planarity : 0.008 0.127 1121 Dihedral : 17.525 179.011 1146 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.09 % Allowed : 31.47 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.92 (0.28), residues: 764 helix: -1.42 (0.31), residues: 223 sheet: -2.34 (0.42), residues: 130 loop : -2.08 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 814 TYR 0.016 0.002 TYR A 393 PHE 0.045 0.002 PHE A 811 TRP 0.010 0.001 TRP A 199 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 6762) covalent geometry : angle 0.74875 / 0.39 ( 9235) SS BOND : bond 0.00106 / 0.07 ( 1) SS BOND : angle 0.60979 / 0.29 ( 2) hydrogen bonds : bond 0.04905 / 3.10 ( 242) hydrogen bonds : angle 6.83280 / 4.66 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.279 Fit side-chains REVERT: A 90 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.3384 (mtm180) REVERT: A 97 ARG cc_start: 0.6926 (mmm-85) cc_final: 0.6444 (ttp-170) REVERT: A 214 MET cc_start: 0.6277 (mtt) cc_final: 0.6051 (mtp) REVERT: A 807 HIS cc_start: 0.4692 (OUTLIER) cc_final: 0.4429 (t70) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.0886 time to fit residues: 10.7138 Evaluate side-chains 80 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.269316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.237260 restraints weight = 8869.802| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 2.61 r_work: 0.4785 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6763 Z= 0.192 Angle : 0.737 8.667 9237 Z= 0.382 Chirality : 0.050 0.371 1041 Planarity : 0.006 0.069 1121 Dihedral : 17.293 177.133 1140 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.03 % Allowed : 28.68 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.72 (0.29), residues: 764 helix: -1.13 (0.32), residues: 224 sheet: -2.50 (0.43), residues: 128 loop : -1.94 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 277 TYR 0.016 0.002 TYR A 667 PHE 0.014 0.002 PHE A 182 TRP 0.008 0.002 TRP A 199 HIS 0.010 0.002 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 6762) covalent geometry : angle 0.73652 / 0.38 ( 9235) SS BOND : bond 0.00551 / 0.34 ( 1) SS BOND : angle 1.45332 / 0.67 ( 2) hydrogen bonds : bond 0.04746 / 3.03 ( 242) hydrogen bonds : angle 6.51380 / 4.48 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6623 (ttp-170) REVERT: A 181 PHE cc_start: 0.6561 (m-80) cc_final: 0.6148 (m-80) REVERT: A 477 ILE cc_start: 0.5331 (OUTLIER) cc_final: 0.4742 (tt) REVERT: A 478 SER cc_start: 0.6812 (OUTLIER) cc_final: 0.6569 (t) REVERT: A 570 LYS cc_start: 0.6122 (mmtm) cc_final: 0.5787 (mmtm) REVERT: A 761 ARG cc_start: 0.5427 (pmt170) cc_final: 0.4901 (pmt170) REVERT: A 807 HIS cc_start: 0.5578 (OUTLIER) cc_final: 0.5157 (m-70) outliers start: 41 outliers final: 22 residues processed: 122 average time/residue: 0.0893 time to fit residues: 14.1660 Evaluate side-chains 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 ASN ** 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 = 0.5155 r_free = 0.5155 target = 0.272584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.240753 restraints weight = 8843.284| |-----------------------------------------------------------------------------| r_work (start): 0.4970 rms_B_bonded: 2.65 r_work: 0.4821 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6763 Z= 0.138 Angle : 0.674 11.204 9237 Z= 0.344 Chirality : 0.048 0.316 1041 Planarity : 0.005 0.049 1121 Dihedral : 17.158 178.278 1140 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.26 % Allowed : 30.00 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.50 (0.30), residues: 764 helix: -0.83 (0.33), residues: 224 sheet: -2.52 (0.43), residues: 128 loop : -1.82 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 506 TYR 0.013 0.001 TYR A 393 PHE 0.020 0.001 PHE A 748 TRP 0.004 0.001 TRP A 451 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6762) covalent geometry : angle 0.67418 / 0.34 ( 9235) SS BOND : bond 0.00278 / 0.17 ( 1) SS BOND : angle 0.75035 / 0.35 ( 2) hydrogen bonds : bond 0.04001 / 2.52 ( 242) hydrogen bonds : angle 6.23212 / 4.30 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6521 (ttp-170) REVERT: A 477 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.4643 (tt) REVERT: A 618 MET cc_start: 0.4301 (mmm) cc_final: 0.4092 (mtp) REVERT: A 639 ILE cc_start: 0.3413 (mm) cc_final: 0.2796 (mm) REVERT: A 780 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6252 (pp30) REVERT: A 807 HIS cc_start: 0.5335 (OUTLIER) cc_final: 0.4866 (m-70) outliers start: 29 outliers final: 22 residues processed: 107 average time/residue: 0.0962 time to fit residues: 13.5276 Evaluate side-chains 100 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.272141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.240226 restraints weight = 8958.327| |-----------------------------------------------------------------------------| r_work (start): 0.4967 rms_B_bonded: 2.64 r_work: 0.4818 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6763 Z= 0.138 Angle : 0.661 8.226 9237 Z= 0.337 Chirality : 0.048 0.299 1041 Planarity : 0.005 0.047 1121 Dihedral : 17.071 178.383 1140 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.44 % Allowed : 29.41 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.37 (0.30), residues: 764 helix: -0.65 (0.33), residues: 226 sheet: -2.53 (0.43), residues: 128 loop : -1.76 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 506 TYR 0.013 0.002 TYR A 393 PHE 0.017 0.001 PHE A 748 TRP 0.004 0.001 TRP A 199 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6762) covalent geometry : angle 0.66088 / 0.34 ( 9235) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.72054 / 0.30 ( 2) hydrogen bonds : bond 0.03886 / 2.47 ( 242) hydrogen bonds : angle 6.07400 / 4.20 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.155 Fit side-chains REVERT: A 97 ARG cc_start: 0.7272 (mmm-85) cc_final: 0.6506 (ttp-170) REVERT: A 214 MET cc_start: 0.6651 (mtt) cc_final: 0.6054 (mtp) REVERT: A 477 ILE cc_start: 0.5382 (OUTLIER) cc_final: 0.4738 (tt) REVERT: A 478 SER cc_start: 0.6790 (OUTLIER) cc_final: 0.6549 (t) REVERT: A 639 ILE cc_start: 0.3489 (mm) cc_final: 0.2904 (mm) REVERT: A 662 THR cc_start: 0.5380 (OUTLIER) cc_final: 0.4651 (t) REVERT: A 746 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3472 (t80) REVERT: A 780 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5872 (pp30) REVERT: A 807 HIS cc_start: 0.5545 (OUTLIER) cc_final: 0.5005 (t70) outliers start: 37 outliers final: 23 residues processed: 111 average time/residue: 0.0819 time to fit residues: 11.9170 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 558 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.270358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.237357 restraints weight = 8978.849| |-----------------------------------------------------------------------------| r_work (start): 0.4934 rms_B_bonded: 2.69 r_work: 0.4787 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6763 Z= 0.168 Angle : 0.686 8.145 9237 Z= 0.349 Chirality : 0.048 0.291 1041 Planarity : 0.005 0.049 1121 Dihedral : 17.044 178.041 1140 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 5.00 % Allowed : 30.29 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.42 (0.30), residues: 764 helix: -0.63 (0.33), residues: 226 sheet: -2.65 (0.42), residues: 128 loop : -1.80 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 792 TYR 0.011 0.002 TYR A 815 PHE 0.018 0.002 PHE A 748 TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6762) covalent geometry : angle 0.68535 / 0.35 ( 9235) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 1.37259 / 0.61 ( 2) hydrogen bonds : bond 0.03991 / 2.60 ( 242) hydrogen bonds : angle 6.06676 / 4.20 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.169 Fit side-chains REVERT: A 355 LYS cc_start: 0.0214 (OUTLIER) cc_final: -0.0907 (tptt) REVERT: A 477 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.4839 (tt) REVERT: A 558 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 570 LYS cc_start: 0.6228 (mmtm) cc_final: 0.5858 (mmtm) REVERT: A 780 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6206 (pp30) REVERT: A 807 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5161 (t70) outliers start: 34 outliers final: 25 residues processed: 111 average time/residue: 0.0830 time to fit residues: 12.2789 Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 761 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 486 GLN A 510 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.272188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.239913 restraints weight = 8854.107| |-----------------------------------------------------------------------------| r_work (start): 0.4960 rms_B_bonded: 2.65 r_work: 0.4810 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6763 Z= 0.139 Angle : 0.658 8.223 9237 Z= 0.336 Chirality : 0.047 0.276 1041 Planarity : 0.005 0.073 1121 Dihedral : 16.987 178.687 1140 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.56 % Allowed : 30.59 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.30 (0.30), residues: 764 helix: -0.53 (0.34), residues: 224 sheet: -2.58 (0.43), residues: 128 loop : -1.72 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 792 TYR 0.009 0.001 TYR A 494 PHE 0.019 0.001 PHE A 181 TRP 0.004 0.001 TRP A 199 HIS 0.003 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6762) covalent geometry : angle 0.65769 / 0.34 ( 9235) SS BOND : bond 0.00104 / 0.06 ( 1) SS BOND : angle 0.93865 / 0.35 ( 2) hydrogen bonds : bond 0.03769 / 2.39 ( 242) hydrogen bonds : angle 5.96289 / 4.14 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.327 Fit side-chains REVERT: A 355 LYS cc_start: 0.0141 (OUTLIER) cc_final: -0.0937 (tptt) REVERT: A 475 ARG cc_start: 0.6433 (ptm160) cc_final: 0.6038 (ptm-80) REVERT: A 662 THR cc_start: 0.5365 (OUTLIER) cc_final: 0.4732 (t) REVERT: A 761 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4600 (pmt170) REVERT: A 780 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5982 (pp30) REVERT: A 807 HIS cc_start: 0.5613 (OUTLIER) cc_final: 0.5077 (t70) outliers start: 31 outliers final: 25 residues processed: 104 average time/residue: 0.0853 time to fit residues: 11.9554 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 761 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 ASN A 548 GLN A 558 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.274024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.242207 restraints weight = 8920.301| |-----------------------------------------------------------------------------| r_work (start): 0.4977 rms_B_bonded: 2.66 r_work: 0.4832 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6763 Z= 0.123 Angle : 0.637 8.297 9237 Z= 0.326 Chirality : 0.047 0.247 1041 Planarity : 0.005 0.070 1121 Dihedral : 16.937 179.120 1140 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.26 % Allowed : 30.74 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.24 (0.30), residues: 764 helix: -0.42 (0.34), residues: 224 sheet: -2.43 (0.40), residues: 143 loop : -1.71 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 506 TYR 0.009 0.001 TYR A 393 PHE 0.016 0.001 PHE A 182 TRP 0.005 0.001 TRP A 199 HIS 0.022 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6762) covalent geometry : angle 0.63667 / 0.33 ( 9235) SS BOND : bond 0.00166 / 0.10 ( 1) SS BOND : angle 0.91632 / 0.32 ( 2) hydrogen bonds : bond 0.03642 / 2.34 ( 242) hydrogen bonds : angle 5.81721 / 4.03 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.241 Fit side-chains REVERT: A 355 LYS cc_start: 0.0148 (OUTLIER) cc_final: -0.0919 (tptt) REVERT: A 475 ARG cc_start: 0.6474 (ptm160) cc_final: 0.6102 (ptm-80) REVERT: A 639 ILE cc_start: 0.3632 (mm) cc_final: 0.3101 (mm) REVERT: A 662 THR cc_start: 0.5389 (OUTLIER) cc_final: 0.4743 (t) REVERT: A 746 PHE cc_start: 0.4313 (OUTLIER) cc_final: 0.3387 (t80) REVERT: A 780 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6181 (pp30) REVERT: A 807 HIS cc_start: 0.5482 (OUTLIER) cc_final: 0.4963 (m-70) outliers start: 29 outliers final: 20 residues processed: 105 average time/residue: 0.0883 time to fit residues: 12.3338 Evaluate side-chains 102 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.270802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.237817 restraints weight = 8875.789| |-----------------------------------------------------------------------------| r_work (start): 0.4946 rms_B_bonded: 2.68 r_work: 0.4795 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6763 Z= 0.158 Angle : 0.664 8.499 9237 Z= 0.339 Chirality : 0.047 0.222 1041 Planarity : 0.005 0.065 1121 Dihedral : 16.905 178.488 1140 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.56 % Allowed : 30.00 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.31 (0.30), residues: 764 helix: -0.44 (0.34), residues: 225 sheet: -2.65 (0.40), residues: 137 loop : -1.73 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 395 TYR 0.010 0.002 TYR A 494 PHE 0.025 0.002 PHE A 182 TRP 0.005 0.001 TRP A 134 HIS 0.004 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 6762) covalent geometry : angle 0.66417 / 0.34 ( 9235) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 0.97078 / 0.39 ( 2) hydrogen bonds : bond 0.03780 / 2.44 ( 242) hydrogen bonds : angle 5.85263 / 4.08 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.177 Fit side-chains REVERT: A 355 LYS cc_start: 0.0199 (OUTLIER) cc_final: -0.0912 (tptt) REVERT: A 475 ARG cc_start: 0.6458 (ptm160) cc_final: 0.6089 (ptm-80) REVERT: A 477 ILE cc_start: 0.5380 (OUTLIER) cc_final: 0.4784 (tt) REVERT: A 662 THR cc_start: 0.5393 (OUTLIER) cc_final: 0.4793 (t) REVERT: A 780 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.6176 (pp30) REVERT: A 807 HIS cc_start: 0.5786 (OUTLIER) cc_final: 0.5213 (t70) outliers start: 31 outliers final: 20 residues processed: 109 average time/residue: 0.0924 time to fit residues: 13.1895 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.273325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.241074 restraints weight = 8854.620| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 2.65 r_work: 0.4825 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6763 Z= 0.131 Angle : 0.653 8.460 9237 Z= 0.333 Chirality : 0.047 0.275 1041 Planarity : 0.005 0.062 1121 Dihedral : 16.890 179.000 1140 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.24 % Allowed : 31.62 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.20 (0.30), residues: 764 helix: -0.33 (0.34), residues: 224 sheet: -2.59 (0.40), residues: 137 loop : -1.67 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 506 TYR 0.012 0.001 TYR A 393 PHE 0.021 0.002 PHE A 182 TRP 0.008 0.001 TRP A 199 HIS 0.024 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 6762) covalent geometry : angle 0.65272 / 0.33 ( 9235) SS BOND : bond 0.00094 / 0.06 ( 1) SS BOND : angle 0.86857 / 0.31 ( 2) hydrogen bonds : bond 0.03579 / 2.29 ( 242) hydrogen bonds : angle 5.77133 / 4.02 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.156 Fit side-chains REVERT: A 104 MET cc_start: 0.7010 (mpp) cc_final: 0.5580 (mtm) REVERT: A 355 LYS cc_start: 0.0232 (OUTLIER) cc_final: -0.0899 (tptt) REVERT: A 475 ARG cc_start: 0.6505 (ptm160) cc_final: 0.6095 (ptm-80) REVERT: A 662 THR cc_start: 0.5356 (OUTLIER) cc_final: 0.4755 (t) REVERT: A 780 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6172 (pp30) REVERT: A 807 HIS cc_start: 0.5608 (OUTLIER) cc_final: 0.5058 (t70) outliers start: 22 outliers final: 18 residues processed: 100 average time/residue: 0.0825 time to fit residues: 10.8605 Evaluate side-chains 100 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 510 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.272146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.239774 restraints weight = 8884.842| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 2.66 r_work: 0.4819 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6763 Z= 0.138 Angle : 0.654 8.306 9237 Z= 0.333 Chirality : 0.047 0.233 1041 Planarity : 0.005 0.059 1121 Dihedral : 16.862 179.101 1140 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.68 % Allowed : 31.32 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.17 (0.30), residues: 764 helix: -0.29 (0.34), residues: 225 sheet: -2.59 (0.40), residues: 137 loop : -1.66 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 366 TYR 0.010 0.001 TYR A 393 PHE 0.030 0.002 PHE A 748 TRP 0.008 0.001 TRP A 199 HIS 0.004 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6762) covalent geometry : angle 0.65374 / 0.33 ( 9235) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.89769 / 0.34 ( 2) hydrogen bonds : bond 0.03586 / 2.31 ( 242) hydrogen bonds : angle 5.72390 / 4.00 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.13 seconds wall clock time: 29 minutes 43.85 seconds (1783.85 seconds total)