Starting phenix.real_space_refine on Thu Jul 2 07:29:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8z_44363/07_2026/9b8z_44363.cif" } resolution = 3.4 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= 0.000 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 V 10 8.30 5 S 39 5.16 5 C 4845 2.51 5 N 1309 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7469 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 4, 'ARG:plan': 14, 'ASP:plan': 16, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 221 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'DVT': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.64, per 1000 atoms: 0.22 Number of scatterers: 7509 At special positions: 0 Unit cell: (95.22, 115.092, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 10 22.97 Ca 2 19.99 S 39 16.00 O 1304 8.00 N 1309 7.00 C 4845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " 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: 0.44 Conformation dependent library (CDL) restraints added in 481.2 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.549A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.797A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.050A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.795A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.618A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1172 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.480A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.303A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 3297 1.45 - 1.67: 4295 1.67 - 1.89: 75 1.89 - 2.11: 28 2.11 - 2.33: 8 Bond restraints: 7703 Sorted by residual: bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CB TRP A 820 " pdb=" CG TRP A 820 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.63e-01 bond pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.81e-01 bond pdb=" CB TRP A 565 " pdb=" CG TRP A 565 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.61e-01 bond pdb=" CB TRP A1124 " pdb=" CG TRP A1124 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.41e-01 ... (remaining 7698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 10147 0.98 - 1.96: 371 1.96 - 2.95: 39 2.95 - 3.93: 31 3.93 - 4.91: 11 Bond angle restraints: 10599 Sorted by residual: angle pdb=" CA TRP A1058 " pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 113.60 109.40 4.20 1.90e+00 2.77e-01 4.89e+00 angle pdb=" C PRO A 340 " pdb=" N LYS A 341 " pdb=" CA LYS A 341 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.51e+00 angle pdb=" C GLY A 306 " pdb=" N ALA A 307 " pdb=" CA ALA A 307 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" C ARG A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta sigma weight residual 122.60 119.09 3.51 1.88e+00 2.83e-01 3.49e+00 angle pdb=" CA TYR A1063 " pdb=" CB TYR A1063 " pdb=" CG TYR A1063 " ideal model delta sigma weight residual 113.90 110.64 3.26 1.80e+00 3.09e-01 3.28e+00 ... (remaining 10594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 4238 15.68 - 31.36: 197 31.36 - 47.04: 53 47.04 - 62.72: 13 62.72 - 78.40: 1 Dihedral angle restraints: 4502 sinusoidal: 1694 harmonic: 2808 Sorted by residual: dihedral pdb=" CA HIS A 447 " pdb=" C HIS A 447 " pdb=" N GLY A 448 " pdb=" CA GLY A 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sinusoidal sigma weight residual -60.00 -117.47 57.47 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG A 571 " pdb=" CB ARG A 571 " pdb=" CG ARG A 571 " pdb=" CD ARG A 571 " ideal model delta sinusoidal sigma weight residual 180.00 125.98 54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 795 0.028 - 0.056: 286 0.056 - 0.084: 73 0.084 - 0.113: 32 0.113 - 0.141: 7 Chirality restraints: 1193 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA PRO A 779 " pdb=" N PRO A 779 " pdb=" C PRO A 779 " pdb=" CB PRO A 779 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL A 188 " pdb=" N VAL A 188 " pdb=" C VAL A 188 " pdb=" CB VAL A 188 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1190 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 457 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 603 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 604 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1029 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C LEU A1029 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU A1029 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A1030 " -0.007 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 60 2.59 - 3.17: 6817 3.17 - 3.75: 11738 3.75 - 4.32: 14991 4.32 - 4.90: 26029 Nonbonded interactions: 59635 Sorted by model distance: nonbonded pdb=" O ARG A 353 " pdb=" OG1 THR A 356 " model vdw 2.014 3.040 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.120 3.250 nonbonded pdb=" NH1 ARG A 195 " pdb=" O PRO A 217 " model vdw 2.209 3.120 nonbonded pdb=" N GLN A 419 " pdb=" OE1 GLN A 419 " model vdw 2.223 3.120 nonbonded pdb=" OE1 GLU A 608 " pdb=" NH1 ARG A 611 " model vdw 2.225 3.120 ... (remaining 59630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.830 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7704 Z= 0.211 Angle : 0.476 4.908 10601 Z= 0.262 Chirality : 0.034 0.141 1193 Planarity : 0.003 0.046 1309 Dihedral : 10.452 78.404 2683 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.54 % Allowed : 4.73 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.29), residues: 958 helix: 2.80 (0.22), residues: 608 sheet: -0.17 (0.80), residues: 50 loop : -0.63 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 892 TYR 0.008 0.001 TYR A1063 PHE 0.012 0.001 PHE A 931 TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 7703) covalent geometry : angle 0.47585 / 0.26 (10599) SS BOND : bond 0.00329 / 0.17 ( 1) SS BOND : angle 0.96705 / 0.56 ( 2) hydrogen bonds : bond 0.12252 / 8.09 ( 473) hydrogen bonds : angle 5.01660 / 3.50 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.295 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8865 (mmm) cc_final: 0.8560 (mmm) REVERT: A 622 MET cc_start: 0.8045 (mtp) cc_final: 0.7655 (mtp) REVERT: A 804 ASP cc_start: 0.7958 (t0) cc_final: 0.7630 (t0) REVERT: A 818 TYR cc_start: 0.8743 (m-10) cc_final: 0.8525 (m-80) REVERT: A 827 GLU cc_start: 0.8275 (tp30) cc_final: 0.8012 (tp30) REVERT: A 877 LEU cc_start: 0.9169 (mt) cc_final: 0.8804 (mt) REVERT: A 884 THR cc_start: 0.9186 (m) cc_final: 0.8636 (p) REVERT: A 1166 ARG cc_start: 0.4523 (ttp80) cc_final: 0.2372 (tpt170) outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 0.0642 time to fit residues: 13.1474 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 831 GLN ** A1017 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 = 0.3420 r_free = 0.3420 target = 0.088927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071862 restraints weight = 21419.045| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.40 r_work: 0.2937 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7704 Z= 0.166 Angle : 0.528 6.496 10601 Z= 0.274 Chirality : 0.038 0.162 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.480 16.037 1072 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.03 % Allowed : 11.35 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.29), residues: 958 helix: 2.82 (0.22), residues: 605 sheet: -0.20 (0.69), residues: 65 loop : -0.54 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.016 0.001 TYR A1168 PHE 0.012 0.001 PHE A 933 TRP 0.010 0.001 TRP A1124 HIS 0.008 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7703) covalent geometry : angle 0.52806 / 0.27 (10599) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.39151 / 0.23 ( 2) hydrogen bonds : bond 0.04180 / 2.94 ( 473) hydrogen bonds : angle 4.23532 / 2.96 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.275 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9134 (m) cc_final: 0.8856 (p) REVERT: A 186 MET cc_start: 0.9268 (mmm) cc_final: 0.8981 (mmm) REVERT: A 254 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8729 (mt-10) REVERT: A 378 LEU cc_start: 0.9447 (mt) cc_final: 0.9219 (mt) REVERT: A 608 GLU cc_start: 0.8507 (tp30) cc_final: 0.8283 (tp30) REVERT: A 804 ASP cc_start: 0.8495 (t0) cc_final: 0.8230 (t0) REVERT: A 818 TYR cc_start: 0.8970 (m-10) cc_final: 0.8681 (m-80) REVERT: A 827 GLU cc_start: 0.8877 (tp30) cc_final: 0.8528 (tp30) REVERT: A 884 THR cc_start: 0.9060 (m) cc_final: 0.8596 (p) REVERT: A 1146 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 1166 ARG cc_start: 0.4911 (ttp80) cc_final: 0.2267 (tpt170) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.0550 time to fit residues: 8.9087 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071728 restraints weight = 21116.136| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.36 r_work: 0.2956 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7704 Z= 0.126 Angle : 0.499 8.860 10601 Z= 0.254 Chirality : 0.037 0.139 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.462 15.827 1072 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.43 % Allowed : 12.84 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 958 helix: 2.84 (0.21), residues: 603 sheet: -0.21 (0.69), residues: 65 loop : -0.71 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.017 0.001 TYR A1168 PHE 0.009 0.001 PHE A 902 TRP 0.010 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7703) covalent geometry : angle 0.49947 / 0.25 (10599) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.44733 / 0.25 ( 2) hydrogen bonds : bond 0.03844 / 2.71 ( 473) hydrogen bonds : angle 4.05496 / 2.83 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.185 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9134 (m) cc_final: 0.8878 (p) REVERT: A 186 MET cc_start: 0.9282 (mmm) cc_final: 0.9024 (mmp) REVERT: A 378 LEU cc_start: 0.9465 (mt) cc_final: 0.9244 (mt) REVERT: A 804 ASP cc_start: 0.8559 (t0) cc_final: 0.8318 (t70) REVERT: A 818 TYR cc_start: 0.9012 (m-10) cc_final: 0.8755 (m-80) REVERT: A 827 GLU cc_start: 0.8829 (tp30) cc_final: 0.8544 (tp30) REVERT: A 833 LEU cc_start: 0.9385 (tp) cc_final: 0.9077 (tt) REVERT: A 884 THR cc_start: 0.9037 (m) cc_final: 0.8551 (p) REVERT: A 900 MET cc_start: 0.9021 (ttp) cc_final: 0.8325 (tpt) REVERT: A 1146 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 1166 ARG cc_start: 0.4909 (ttp80) cc_final: 0.2272 (tpt170) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.0550 time to fit residues: 9.2668 Evaluate side-chains 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.0470 chunk 26 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072923 restraints weight = 21431.062| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.39 r_work: 0.2979 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7704 Z= 0.103 Angle : 0.486 8.317 10601 Z= 0.243 Chirality : 0.036 0.132 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.429 16.056 1072 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.57 % Allowed : 15.27 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 958 helix: 2.81 (0.21), residues: 600 sheet: -0.19 (0.69), residues: 65 loop : -0.80 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.017 0.001 TYR A1168 PHE 0.020 0.001 PHE A 902 TRP 0.009 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7703) covalent geometry : angle 0.48565 / 0.24 (10599) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.36363 / 0.20 ( 2) hydrogen bonds : bond 0.03557 / 2.51 ( 473) hydrogen bonds : angle 3.92373 / 2.74 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.212 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9135 (m) cc_final: 0.8850 (p) REVERT: A 186 MET cc_start: 0.9267 (mmm) cc_final: 0.9016 (mmp) REVERT: A 355 MET cc_start: 0.9619 (mmp) cc_final: 0.9347 (mmm) REVERT: A 378 LEU cc_start: 0.9475 (mt) cc_final: 0.9263 (mt) REVERT: A 608 GLU cc_start: 0.8685 (mp0) cc_final: 0.8394 (mp0) REVERT: A 804 ASP cc_start: 0.8558 (t0) cc_final: 0.8314 (t70) REVERT: A 818 TYR cc_start: 0.8988 (m-10) cc_final: 0.8742 (m-80) REVERT: A 827 GLU cc_start: 0.8866 (tp30) cc_final: 0.8523 (tp30) REVERT: A 884 THR cc_start: 0.8971 (m) cc_final: 0.8490 (p) REVERT: A 900 MET cc_start: 0.8969 (ttp) cc_final: 0.8270 (tpt) REVERT: A 1146 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 1166 ARG cc_start: 0.4888 (ttp80) cc_final: 0.2311 (tpt170) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 0.0543 time to fit residues: 9.2675 Evaluate side-chains 104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.069303 restraints weight = 21515.314| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.32 r_work: 0.2904 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7704 Z= 0.222 Angle : 0.580 7.541 10601 Z= 0.287 Chirality : 0.039 0.128 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.535 16.924 1072 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.24 % Allowed : 15.27 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.29), residues: 958 helix: 2.75 (0.21), residues: 602 sheet: -0.28 (0.68), residues: 63 loop : -0.91 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 771 TYR 0.018 0.001 TYR A1168 PHE 0.015 0.001 PHE A 933 TRP 0.011 0.001 TRP A1124 HIS 0.007 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 7703) covalent geometry : angle 0.57978 / 0.29 (10599) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.71481 / 0.42 ( 2) hydrogen bonds : bond 0.04065 / 2.87 ( 473) hydrogen bonds : angle 4.13496 / 2.90 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.242 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9188 (m) cc_final: 0.8896 (p) REVERT: A 608 GLU cc_start: 0.8851 (mp0) cc_final: 0.8498 (mp0) REVERT: A 818 TYR cc_start: 0.9053 (m-10) cc_final: 0.8820 (m-80) REVERT: A 827 GLU cc_start: 0.9007 (tp30) cc_final: 0.8686 (tp30) REVERT: A 884 THR cc_start: 0.9075 (m) cc_final: 0.8346 (p) REVERT: A 900 MET cc_start: 0.9008 (ttp) cc_final: 0.8318 (tpt) REVERT: A 984 ASP cc_start: 0.8593 (t70) cc_final: 0.8390 (t0) REVERT: A 1146 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 1166 ARG cc_start: 0.5043 (ttp80) cc_final: 0.2321 (tpt170) outliers start: 24 outliers final: 14 residues processed: 108 average time/residue: 0.0561 time to fit residues: 9.0082 Evaluate side-chains 99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071430 restraints weight = 21290.561| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.37 r_work: 0.2949 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7704 Z= 0.117 Angle : 0.507 7.794 10601 Z= 0.250 Chirality : 0.037 0.126 1193 Planarity : 0.004 0.050 1309 Dihedral : 3.461 16.868 1072 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.70 % Allowed : 15.54 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.29), residues: 958 helix: 2.80 (0.21), residues: 601 sheet: -0.35 (0.68), residues: 64 loop : -0.93 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.018 0.001 TYR A1168 PHE 0.011 0.001 PHE A 902 TRP 0.009 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7703) covalent geometry : angle 0.50718 / 0.25 (10599) SS BOND : bond 0.00094 / 0.05 ( 1) SS BOND : angle 0.48218 / 0.28 ( 2) hydrogen bonds : bond 0.03659 / 2.58 ( 473) hydrogen bonds : angle 3.96012 / 2.76 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.301 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9173 (m) cc_final: 0.8877 (p) REVERT: A 608 GLU cc_start: 0.8873 (mp0) cc_final: 0.8542 (mp0) REVERT: A 818 TYR cc_start: 0.9004 (m-10) cc_final: 0.8786 (m-80) REVERT: A 827 GLU cc_start: 0.8955 (tp30) cc_final: 0.8585 (tp30) REVERT: A 884 THR cc_start: 0.8985 (m) cc_final: 0.8495 (p) REVERT: A 900 MET cc_start: 0.8979 (ttp) cc_final: 0.8283 (tpt) REVERT: A 1166 ARG cc_start: 0.5097 (ttp80) cc_final: 0.2435 (tpt170) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.0538 time to fit residues: 8.8764 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 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 = 0.3396 r_free = 0.3396 target = 0.087120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070232 restraints weight = 21409.883| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.36 r_work: 0.2927 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7704 Z= 0.154 Angle : 0.528 8.571 10601 Z= 0.260 Chirality : 0.037 0.126 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.435 16.198 1072 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.30 % Allowed : 17.30 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.29), residues: 958 helix: 2.77 (0.21), residues: 601 sheet: -0.42 (0.69), residues: 64 loop : -0.96 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.018 0.001 TYR A1168 PHE 0.010 0.001 PHE A 627 TRP 0.010 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7703) covalent geometry : angle 0.52795 / 0.26 (10599) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 0.56998 / 0.33 ( 2) hydrogen bonds : bond 0.03715 / 2.62 ( 473) hydrogen bonds : angle 4.00313 / 2.80 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.184 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9211 (m) cc_final: 0.8908 (p) REVERT: A 608 GLU cc_start: 0.8896 (mp0) cc_final: 0.8555 (mp0) REVERT: A 818 TYR cc_start: 0.9035 (m-10) cc_final: 0.8818 (m-80) REVERT: A 827 GLU cc_start: 0.9011 (tp30) cc_final: 0.8661 (tp30) REVERT: A 884 THR cc_start: 0.8981 (m) cc_final: 0.8490 (p) REVERT: A 900 MET cc_start: 0.8985 (ttp) cc_final: 0.8250 (tpt) REVERT: A 1166 ARG cc_start: 0.5143 (ttp80) cc_final: 0.2458 (tpt170) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.0619 time to fit residues: 8.9712 Evaluate side-chains 95 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.0270 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 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 = 0.3424 r_free = 0.3424 target = 0.088703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071793 restraints weight = 21481.176| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.38 r_work: 0.2955 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7704 Z= 0.111 Angle : 0.519 10.326 10601 Z= 0.251 Chirality : 0.036 0.140 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.406 14.896 1072 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 17.84 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.29), residues: 958 helix: 2.79 (0.21), residues: 601 sheet: -0.45 (0.68), residues: 64 loop : -0.98 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.019 0.001 TYR A1168 PHE 0.009 0.001 PHE A 902 TRP 0.009 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7703) covalent geometry : angle 0.51862 / 0.25 (10599) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.46126 / 0.26 ( 2) hydrogen bonds : bond 0.03507 / 2.47 ( 473) hydrogen bonds : angle 3.89543 / 2.72 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.289 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9164 (m) cc_final: 0.8854 (p) REVERT: A 430 MET cc_start: 0.9383 (mmm) cc_final: 0.9020 (tpp) REVERT: A 608 GLU cc_start: 0.8881 (mp0) cc_final: 0.8539 (mp0) REVERT: A 644 ARG cc_start: 0.5798 (mmt180) cc_final: 0.5441 (tpt170) REVERT: A 827 GLU cc_start: 0.8968 (tp30) cc_final: 0.8583 (tp30) REVERT: A 900 MET cc_start: 0.8941 (ttp) cc_final: 0.8192 (tpt) REVERT: A 1166 ARG cc_start: 0.5212 (ttp80) cc_final: 0.2523 (tpt170) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.0636 time to fit residues: 9.6753 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072194 restraints weight = 21118.654| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.37 r_work: 0.2972 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7704 Z= 0.112 Angle : 0.520 11.350 10601 Z= 0.252 Chirality : 0.036 0.125 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.370 13.634 1072 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.57 % Allowed : 17.84 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.29), residues: 958 helix: 2.79 (0.21), residues: 601 sheet: -0.53 (0.68), residues: 64 loop : -0.96 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.030 0.001 TYR A 818 PHE 0.010 0.001 PHE A 373 TRP 0.012 0.001 TRP A 403 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7703) covalent geometry : angle 0.52041 / 0.25 (10599) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 0.50029 / 0.29 ( 2) hydrogen bonds : bond 0.03455 / 2.43 ( 473) hydrogen bonds : angle 3.89369 / 2.72 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.253 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9138 (m) cc_final: 0.8827 (p) REVERT: A 430 MET cc_start: 0.9299 (mmm) cc_final: 0.9026 (tpp) REVERT: A 608 GLU cc_start: 0.8890 (mp0) cc_final: 0.8573 (mp0) REVERT: A 644 ARG cc_start: 0.5819 (mmt180) cc_final: 0.5337 (tpt170) REVERT: A 827 GLU cc_start: 0.8991 (tp30) cc_final: 0.8592 (tp30) REVERT: A 900 MET cc_start: 0.8937 (ttp) cc_final: 0.8160 (tpt) REVERT: A 1166 ARG cc_start: 0.5204 (ttp80) cc_final: 0.2507 (tpt170) outliers start: 19 outliers final: 17 residues processed: 100 average time/residue: 0.0603 time to fit residues: 9.1124 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 0.0070 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072997 restraints weight = 21157.943| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.39 r_work: 0.2980 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7704 Z= 0.103 Angle : 0.534 9.890 10601 Z= 0.257 Chirality : 0.039 0.355 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.357 13.194 1072 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.43 % Allowed : 18.38 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.29), residues: 958 helix: 2.74 (0.21), residues: 604 sheet: -0.54 (0.68), residues: 64 loop : -0.93 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1138 TYR 0.019 0.001 TYR A1168 PHE 0.009 0.001 PHE A 627 TRP 0.009 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7703) covalent geometry : angle 0.53365 / 0.26 (10599) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.49544 / 0.28 ( 2) hydrogen bonds : bond 0.03361 / 2.35 ( 473) hydrogen bonds : angle 3.90161 / 2.74 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.216 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9104 (m) cc_final: 0.8791 (p) REVERT: A 430 MET cc_start: 0.9263 (mmm) cc_final: 0.9031 (tpp) REVERT: A 608 GLU cc_start: 0.8879 (mp0) cc_final: 0.8571 (mp0) REVERT: A 644 ARG cc_start: 0.5802 (mmt180) cc_final: 0.5322 (tpt170) REVERT: A 827 GLU cc_start: 0.8970 (tp30) cc_final: 0.8582 (tp30) REVERT: A 900 MET cc_start: 0.8913 (ttp) cc_final: 0.8122 (tpt) REVERT: A 1166 ARG cc_start: 0.5251 (ttp80) cc_final: 0.2553 (tpt170) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.0693 time to fit residues: 10.3217 Evaluate side-chains 95 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.088721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071849 restraints weight = 21151.276| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.37 r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7704 Z= 0.135 Angle : 0.557 12.519 10601 Z= 0.267 Chirality : 0.041 0.443 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.370 13.342 1072 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.30 % Allowed : 19.05 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.29), residues: 958 helix: 2.73 (0.21), residues: 603 sheet: -0.61 (0.68), residues: 64 loop : -0.94 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.019 0.001 TYR A1168 PHE 0.010 0.001 PHE A 627 TRP 0.009 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7703) covalent geometry : angle 0.55687 / 0.27 (10599) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.58036 / 0.33 ( 2) hydrogen bonds : bond 0.03460 / 2.42 ( 473) hydrogen bonds : angle 3.96127 / 2.78 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.75 seconds wall clock time: 27 minutes 36.57 seconds (1656.57 seconds total)