Starting phenix.real_space_refine on Thu Jul 2 04:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6p_62131/07_2026/9k6p_62131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6p_62131/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2026/9k6p_62131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2026/9k6p_62131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2026/9k6p_62131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6p_62131/07_2026/9k6p_62131.map" } 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): 0.01s 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: 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: 1.27, per 1000 atoms: 0.19 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: 0.62 Conformation dependent library (CDL) restraints added in 394.5 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: 0.47 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: 0.83 Time building geometry restraints manager: 0.82 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: 914 0.099 - 0.197: 105 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: 0.390 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.200 ------------------------------------------------------------------------------- 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= 0.395 Angle : 1.430 39.033 9237 Z= 0.816 Chirality : 0.072 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 / 0.39 ( 6762) covalent geometry : angle 1.42939 / 0.82 ( 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 : 0.193 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: 0.0968 time to fit residues: 10.9528 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 : 0.194 ------------------------------------------------------------------------------- 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 = 0.5188 r_free = 0.5188 target = 0.277011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.247380 restraints weight = 8891.917| |-----------------------------------------------------------------------------| r_work (start): 0.5014 rms_B_bonded: 2.58 r_work: 0.4873 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 6763 Z= 0.154 Angle : 0.732 8.090 9237 Z= 0.386 Chirality : 0.049 0.222 1041 Planarity : 0.008 0.137 1121 Dihedral : 17.690 178.567 1146 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.38 % Allowed : 31.18 % 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: -2.93 (0.28), residues: 764 helix: -1.43 (0.31), residues: 222 sheet: -2.34 (0.42), residues: 130 loop : -2.09 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.019 0.002 TYR A 393 PHE 0.043 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 0.73247 / 0.39 ( 9235) SS BOND : bond 0.00093 / 0.06 ( 1) SS BOND : angle 0.59931 / 0.28 ( 2) hydrogen bonds : bond 0.04900 / 3.11 ( 242) hydrogen bonds : angle 6.85053 / 4.68 ( 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 97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.132 Fit side-chains REVERT: A 97 ARG cc_start: 0.6886 (mmm-85) cc_final: 0.6443 (ttp-170) REVERT: A 209 SER cc_start: 0.5539 (OUTLIER) cc_final: 0.5263 (t) REVERT: A 214 MET cc_start: 0.6320 (mtt) cc_final: 0.6083 (mtp) REVERT: A 504 MET cc_start: 0.6345 (mpt) cc_final: 0.6019 (mpt) REVERT: A 807 HIS cc_start: 0.4680 (OUTLIER) cc_final: 0.4411 (t70) outliers start: 23 outliers final: 12 residues processed: 93 average time/residue: 0.0796 time to fit residues: 9.6493 Evaluate side-chains 82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 209 SER 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 752 SER 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: 8.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 66 optimal weight: 0.0870 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 HIS ** 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 = 0.5167 r_free = 0.5167 target = 0.272470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.244023 restraints weight = 8646.443| |-----------------------------------------------------------------------------| r_work (start): 0.4989 rms_B_bonded: 2.46 r_work: 0.4852 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6763 Z= 0.146 Angle : 0.668 7.474 9237 Z= 0.351 Chirality : 0.047 0.221 1041 Planarity : 0.006 0.051 1121 Dihedral : 17.466 179.351 1140 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.56 % Allowed : 29.56 % Favored : 65.88 % 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: -2.57 (0.29), residues: 764 helix: -1.01 (0.32), residues: 224 sheet: -2.32 (0.44), residues: 128 loop : -1.88 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.008 0.001 TYR A 494 PHE 0.011 0.001 PHE A 182 TRP 0.006 0.001 TRP A 199 HIS 0.005 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6762) covalent geometry : angle 0.66811 / 0.35 ( 9235) SS BOND : bond 0.00441 / 0.28 ( 1) SS BOND : angle 1.04451 / 0.49 ( 2) hydrogen bonds : bond 0.04287 / 2.73 ( 242) hydrogen bonds : angle 6.39132 / 4.39 ( 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 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.196 Fit side-chains REVERT: A 97 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6573 (ttp-170) REVERT: A 418 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5083 (pp) REVERT: A 477 ILE cc_start: 0.5169 (OUTLIER) cc_final: 0.4501 (tt) REVERT: A 494 TYR cc_start: 0.5673 (m-10) cc_final: 0.5450 (m-10) REVERT: A 549 MET cc_start: 0.5462 (mpp) cc_final: 0.5242 (mpp) REVERT: A 780 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5863 (pp30) REVERT: A 807 HIS cc_start: 0.5095 (OUTLIER) cc_final: 0.4699 (m-70) outliers start: 31 outliers final: 16 residues processed: 104 average time/residue: 0.0688 time to fit residues: 9.4839 Evaluate side-chains 92 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 418 ILE 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 744 THR Chi-restraints excluded: chain A residue 752 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 551 ASN A 711 HIS ** 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 = 0.5178 r_free = 0.5178 target = 0.275130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.244226 restraints weight = 8838.515| |-----------------------------------------------------------------------------| r_work (start): 0.4986 rms_B_bonded: 2.60 r_work: 0.4847 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6763 Z= 0.132 Angle : 0.648 7.547 9237 Z= 0.338 Chirality : 0.047 0.224 1041 Planarity : 0.005 0.047 1121 Dihedral : 17.372 179.247 1140 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.15 % Allowed : 28.68 % Favored : 66.18 % 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: -2.38 (0.30), residues: 764 helix: -0.71 (0.33), residues: 224 sheet: -2.33 (0.44), residues: 128 loop : -1.81 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.008 0.001 TYR A 174 PHE 0.010 0.001 PHE A 200 TRP 0.004 0.001 TRP A 134 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6762) covalent geometry : angle 0.64797 / 0.34 ( 9235) SS BOND : bond 0.00168 / 0.11 ( 1) SS BOND : angle 0.76326 / 0.28 ( 2) hydrogen bonds : bond 0.03858 / 2.46 ( 242) hydrogen bonds : angle 6.13809 / 4.23 ( 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.257 Fit side-chains REVERT: A 97 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6616 (ttp-170) REVERT: A 477 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.4700 (tt) REVERT: A 478 SER cc_start: 0.6717 (OUTLIER) cc_final: 0.6503 (t) REVERT: A 639 ILE cc_start: 0.3371 (mm) cc_final: 0.2715 (mm) REVERT: A 780 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5975 (pp30) REVERT: A 807 HIS cc_start: 0.5177 (OUTLIER) cc_final: 0.4738 (m-70) outliers start: 35 outliers final: 19 residues processed: 109 average time/residue: 0.0668 time to fit residues: 9.8468 Evaluate side-chains 92 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 371 SER Chi-restraints excluded: chain A residue 390 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 680 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 711 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 0.0000 chunk 73 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.5159 r_free = 0.5159 target = 0.272729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.241155 restraints weight = 9017.399| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 2.65 r_work: 0.4822 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.1955 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= 0.147 Angle : 0.657 7.797 9237 Z= 0.342 Chirality : 0.047 0.232 1041 Planarity : 0.005 0.047 1121 Dihedral : 17.300 179.030 1140 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.00 % Allowed : 29.12 % Favored : 65.88 % 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: -2.34 (0.30), residues: 764 helix: -0.66 (0.33), residues: 225 sheet: -2.40 (0.43), residues: 128 loop : -1.76 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 366 TYR 0.011 0.002 TYR A 393 PHE 0.009 0.001 PHE A 200 TRP 0.004 0.001 TRP A 134 HIS 0.008 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6762) covalent geometry : angle 0.65725 / 0.34 ( 9235) SS BOND : bond 0.00250 / 0.16 ( 1) SS BOND : angle 1.26053 / 0.54 ( 2) hydrogen bonds : bond 0.03863 / 2.45 ( 242) hydrogen bonds : angle 6.05682 / 4.18 ( 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 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.210 Fit side-chains REVERT: A 97 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6549 (ttp-170) REVERT: A 477 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.4694 (tt) REVERT: A 478 SER cc_start: 0.6832 (OUTLIER) cc_final: 0.6597 (t) REVERT: A 639 ILE cc_start: 0.3419 (mm) cc_final: 0.2805 (mm) REVERT: A 780 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6145 (pp30) REVERT: A 807 HIS cc_start: 0.5283 (OUTLIER) cc_final: 0.4836 (m-70) outliers start: 34 outliers final: 21 residues processed: 105 average time/residue: 0.0753 time to fit residues: 10.6162 Evaluate side-chains 98 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 390 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 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 Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5166 r_free = 0.5166 target = 0.273578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.241816 restraints weight = 8979.150| |-----------------------------------------------------------------------------| r_work (start): 0.4969 rms_B_bonded: 2.68 r_work: 0.4825 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6763 Z= 0.134 Angle : 0.647 8.097 9237 Z= 0.334 Chirality : 0.047 0.221 1041 Planarity : 0.005 0.046 1121 Dihedral : 17.261 179.229 1140 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.15 % Allowed : 28.24 % Favored : 66.62 % 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: -2.27 (0.30), residues: 764 helix: -0.59 (0.33), residues: 226 sheet: -2.42 (0.43), residues: 128 loop : -1.70 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 366 TYR 0.012 0.001 TYR A 815 PHE 0.013 0.001 PHE A 182 TRP 0.005 0.001 TRP A 435 HIS 0.003 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 6762) covalent geometry : angle 0.64701 / 0.33 ( 9235) SS BOND : bond 0.00210 / 0.13 ( 1) SS BOND : angle 1.13920 / 0.43 ( 2) hydrogen bonds : bond 0.03735 / 2.39 ( 242) hydrogen bonds : angle 5.93035 / 4.10 ( 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 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.213 Fit side-chains REVERT: A 97 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6653 (ttp-170) REVERT: A 477 ILE cc_start: 0.5447 (OUTLIER) cc_final: 0.4793 (tt) REVERT: A 639 ILE cc_start: 0.3488 (mm) cc_final: 0.2883 (mm) REVERT: A 780 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.6139 (pp30) REVERT: A 807 HIS cc_start: 0.5480 (OUTLIER) cc_final: 0.5012 (m-70) outliers start: 35 outliers final: 24 residues processed: 109 average time/residue: 0.0658 time to fit residues: 9.6822 Evaluate side-chains 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 209 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 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 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 757 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 558 GLN ** 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 = 0.5157 r_free = 0.5157 target = 0.272835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.240625 restraints weight = 8841.988| |-----------------------------------------------------------------------------| r_work (start): 0.4965 rms_B_bonded: 2.65 r_work: 0.4815 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6763 Z= 0.150 Angle : 0.649 8.299 9237 Z= 0.336 Chirality : 0.047 0.232 1041 Planarity : 0.005 0.046 1121 Dihedral : 17.203 179.111 1140 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.71 % Allowed : 29.26 % Favored : 66.03 % 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: -2.27 (0.30), residues: 764 helix: -0.57 (0.33), residues: 226 sheet: -2.48 (0.43), residues: 128 loop : -1.69 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 792 TYR 0.011 0.002 TYR A 804 PHE 0.013 0.001 PHE A 182 TRP 0.005 0.001 TRP A 435 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6762) covalent geometry : angle 0.64846 / 0.34 ( 9235) SS BOND : bond 0.00198 / 0.12 ( 1) SS BOND : angle 1.18352 / 0.44 ( 2) hydrogen bonds : bond 0.03722 / 2.37 ( 242) hydrogen bonds : angle 5.88693 / 4.07 ( 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 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.173 Fit side-chains REVERT: A 97 ARG cc_start: 0.7187 (mmm-85) cc_final: 0.6548 (ttp-170) REVERT: A 477 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.4869 (tt) REVERT: A 662 THR cc_start: 0.5421 (OUTLIER) cc_final: 0.4700 (t) REVERT: A 780 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6137 (pp30) REVERT: A 807 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.5069 (t70) outliers start: 32 outliers final: 24 residues processed: 107 average time/residue: 0.0740 time to fit residues: 10.4877 Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 203 HIS 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 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 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 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: 0.5980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** A 558 GLN ** 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 = 0.5167 r_free = 0.5167 target = 0.274076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.242192 restraints weight = 8922.436| |-----------------------------------------------------------------------------| r_work (start): 0.4976 rms_B_bonded: 2.66 r_work: 0.4828 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6763 Z= 0.130 Angle : 0.640 8.307 9237 Z= 0.331 Chirality : 0.047 0.230 1041 Planarity : 0.005 0.075 1121 Dihedral : 17.140 179.424 1140 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.12 % Allowed : 30.59 % 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: -2.15 (0.30), residues: 764 helix: -0.46 (0.34), residues: 224 sheet: -2.18 (0.44), residues: 129 loop : -1.71 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 506 TYR 0.009 0.001 TYR A 393 PHE 0.019 0.001 PHE A 181 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 0.00302 / 0.13 ( 6762) covalent geometry : angle 0.63949 / 0.33 ( 9235) SS BOND : bond 0.00244 / 0.15 ( 1) SS BOND : angle 1.17045 / 0.42 ( 2) hydrogen bonds : bond 0.03602 / 2.31 ( 242) hydrogen bonds : angle 5.80740 / 4.02 ( 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: 28 poor density : 79 time to evaluate : 0.206 Fit side-chains REVERT: A 97 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6534 (ttp-170) REVERT: A 639 ILE cc_start: 0.3595 (mm) cc_final: 0.3076 (mm) REVERT: A 662 THR cc_start: 0.5389 (OUTLIER) cc_final: 0.4689 (t) REVERT: A 780 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.6124 (pp30) REVERT: A 807 HIS cc_start: 0.5508 (OUTLIER) cc_final: 0.4999 (t70) outliers start: 28 outliers final: 22 residues processed: 104 average time/residue: 0.0749 time to fit residues: 10.1946 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 : 0.162 ------------------------------------------------------------------------------- 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 209 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 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 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 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: 4.9990 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 558 GLN ** 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 = 0.5141 r_free = 0.5141 target = 0.271339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.238885 restraints weight = 8883.622| |-----------------------------------------------------------------------------| r_work (start): 0.4952 rms_B_bonded: 2.64 r_work: 0.4800 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6763 Z= 0.154 Angle : 0.660 8.404 9237 Z= 0.341 Chirality : 0.047 0.229 1041 Planarity : 0.006 0.071 1121 Dihedral : 17.013 178.928 1140 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.85 % Allowed : 29.85 % 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: -2.22 (0.30), residues: 764 helix: -0.53 (0.33), residues: 225 sheet: -2.36 (0.44), residues: 123 loop : -1.71 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 506 TYR 0.011 0.002 TYR A 804 PHE 0.017 0.002 PHE A 181 TRP 0.005 0.001 TRP A 199 HIS 0.004 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 6762) covalent geometry : angle 0.65976 / 0.34 ( 9235) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 1.17806 / 0.45 ( 2) hydrogen bonds : bond 0.03679 / 2.37 ( 242) hydrogen bonds : angle 5.82478 / 4.04 ( 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.255 Fit side-chains REVERT: A 86 ILE cc_start: 0.4379 (mp) cc_final: 0.4004 (mm) REVERT: A 104 MET cc_start: 0.7006 (mpp) cc_final: 0.5991 (mtt) REVERT: A 182 PHE cc_start: 0.4527 (m-10) cc_final: 0.4245 (m-80) REVERT: A 477 ILE cc_start: 0.5482 (OUTLIER) cc_final: 0.4873 (tt) REVERT: A 558 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: A 662 THR cc_start: 0.5442 (OUTLIER) cc_final: 0.4790 (t) REVERT: A 780 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6182 (pp30) REVERT: A 807 HIS cc_start: 0.5689 (OUTLIER) cc_final: 0.5144 (t70) outliers start: 33 outliers final: 23 residues processed: 108 average time/residue: 0.0671 time to fit residues: 9.6596 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 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 555 THR Chi-restraints excluded: chain A residue 558 GLN 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 Chi-restraints excluded: chain A residue 856 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 510 ASN 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 = 0.5152 r_free = 0.5152 target = 0.272765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.240434 restraints weight = 8861.444| |-----------------------------------------------------------------------------| r_work (start): 0.4965 rms_B_bonded: 2.64 r_work: 0.4815 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6763 Z= 0.135 Angle : 0.650 8.301 9237 Z= 0.335 Chirality : 0.047 0.223 1041 Planarity : 0.006 0.070 1121 Dihedral : 16.970 179.168 1140 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.41 % Allowed : 30.00 % Favored : 65.59 % 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: -2.19 (0.30), residues: 764 helix: -0.48 (0.34), residues: 225 sheet: -2.30 (0.42), residues: 134 loop : -1.68 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 366 TYR 0.012 0.001 TYR A 393 PHE 0.017 0.001 PHE A 181 TRP 0.008 0.001 TRP A 199 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6762) covalent geometry : angle 0.64971 / 0.33 ( 9235) SS BOND : bond 0.00177 / 0.11 ( 1) SS BOND : angle 1.53606 / 0.56 ( 2) hydrogen bonds : bond 0.03577 / 2.27 ( 242) hydrogen bonds : angle 5.78507 / 4.01 ( 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 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.164 Fit side-chains REVERT: A 86 ILE cc_start: 0.4557 (mp) cc_final: 0.4326 (mm) REVERT: A 104 MET cc_start: 0.6819 (mpp) cc_final: 0.5813 (mtt) REVERT: A 477 ILE cc_start: 0.5445 (OUTLIER) cc_final: 0.4839 (tt) REVERT: A 662 THR cc_start: 0.5433 (OUTLIER) cc_final: 0.4781 (t) REVERT: A 780 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6204 (pp30) REVERT: A 807 HIS cc_start: 0.5627 (OUTLIER) cc_final: 0.5100 (t70) outliers start: 30 outliers final: 23 residues processed: 101 average time/residue: 0.0659 time to fit residues: 8.8079 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 390 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 555 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.272049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.239787 restraints weight = 8892.900| |-----------------------------------------------------------------------------| r_work (start): 0.4963 rms_B_bonded: 2.64 r_work: 0.4815 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6763 Z= 0.141 Angle : 0.649 8.185 9237 Z= 0.335 Chirality : 0.047 0.221 1041 Planarity : 0.006 0.068 1121 Dihedral : 16.922 179.190 1140 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.97 % Allowed : 30.59 % 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: -2.17 (0.30), residues: 764 helix: -0.43 (0.34), residues: 224 sheet: -2.28 (0.41), residues: 138 loop : -1.69 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 366 TYR 0.013 0.002 TYR A 393 PHE 0.019 0.002 PHE A 182 TRP 0.009 0.001 TRP A 199 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6762) covalent geometry : angle 0.64852 / 0.33 ( 9235) SS BOND : bond 0.00165 / 0.10 ( 1) SS BOND : angle 1.45147 / 0.53 ( 2) hydrogen bonds : bond 0.03560 / 2.28 ( 242) hydrogen bonds : angle 5.76263 / 3.99 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1358.51 seconds wall clock time: 24 minutes 6.30 seconds (1446.30 seconds total)