Starting phenix.real_space_refine on Wed Sep 17 09:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8z_44363/09_2025/9b8z_44363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8z_44363/09_2025/9b8z_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_44363/09_2025/9b8z_44363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8z_44363/09_2025/9b8z_44363.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8z_44363/09_2025/9b8z_44363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8z_44363/09_2025/9b8z_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-2.0-5805/lib/python3.9/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, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.87, per 1000 atoms: 0.25 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: 0.59 Conformation dependent library (CDL) restraints added in 541.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.37 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: 1.46 Time building geometry restraints manager: 0.81 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 2.510 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: 4.200 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 aren 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 covalent geometry : bond 0.00446 ( 7703) covalent geometry : angle 0.47585 (10599) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.96705 ( 2) hydrogen bonds : bond 0.12252 ( 473) hydrogen bonds : angle 5.01660 ( 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 : 0.331 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: 0.8561 (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: 0.0768 time to fit residues: 15.3760 Evaluate side-chains 99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 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 = 0.3419 r_free = 0.3419 target = 0.088999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071968 restraints weight = 21432.601| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.39 r_work: 0.2939 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7704 Z= 0.166 Angle : 0.529 6.436 10601 Z= 0.274 Chirality : 0.039 0.170 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.490 16.109 1072 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.16 % Allowed : 11.08 % Favored : 86.76 % 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 aren not related in a simple way. whole: 2.47 (0.29), residues: 958 helix: 2.82 (0.22), residues: 605 sheet: -0.23 (0.69), residues: 65 loop : -0.55 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 612 TYR 0.015 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 covalent geometry : bond 0.00367 ( 7703) covalent geometry : angle 0.52912 (10599) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.42244 ( 2) hydrogen bonds : bond 0.04121 ( 473) hydrogen bonds : angle 4.22304 ( 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 119 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.292 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9133 (m) cc_final: 0.8857 (p) REVERT: A 186 MET cc_start: 0.9270 (mmm) cc_final: 0.8984 (mmm) REVERT: A 254 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8840 (mt-10) REVERT: A 378 LEU cc_start: 0.9452 (mt) cc_final: 0.9224 (mt) REVERT: A 608 GLU cc_start: 0.8497 (tp30) cc_final: 0.8276 (tp30) REVERT: A 804 ASP cc_start: 0.8513 (t0) cc_final: 0.8256 (t0) REVERT: A 818 TYR cc_start: 0.8972 (m-10) cc_final: 0.8682 (m-80) REVERT: A 827 GLU cc_start: 0.8911 (tp30) cc_final: 0.8552 (tp30) REVERT: A 884 THR cc_start: 0.9058 (m) cc_final: 0.8595 (p) REVERT: A 1146 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 1166 ARG cc_start: 0.4945 (ttp80) cc_final: 0.2287 (tpt170) outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 0.0716 time to fit residues: 11.8664 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3421 r_free = 0.3421 target = 0.088879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071902 restraints weight = 21077.549| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.37 r_work: 0.2953 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7704 Z= 0.129 Angle : 0.499 8.500 10601 Z= 0.253 Chirality : 0.037 0.139 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.468 15.846 1072 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.97 % Allowed : 12.57 % Favored : 84.46 % 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 aren not related in a simple way. whole: 2.41 (0.29), residues: 958 helix: 2.85 (0.21), residues: 602 sheet: -0.24 (0.69), residues: 65 loop : -0.74 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 612 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 covalent geometry : bond 0.00292 ( 7703) covalent geometry : angle 0.49922 (10599) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.46279 ( 2) hydrogen bonds : bond 0.03845 ( 473) hydrogen bonds : angle 4.06448 ( 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 122 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.307 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9128 (m) cc_final: 0.8869 (p) REVERT: A 186 MET cc_start: 0.9294 (mmm) cc_final: 0.9032 (mmp) REVERT: A 254 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8834 (mt-10) REVERT: A 378 LEU cc_start: 0.9472 (mt) cc_final: 0.9252 (mt) REVERT: A 818 TYR cc_start: 0.9025 (m-10) cc_final: 0.8765 (m-80) REVERT: A 827 GLU cc_start: 0.8826 (tp30) cc_final: 0.8501 (tp30) REVERT: A 884 THR cc_start: 0.9036 (m) cc_final: 0.8552 (p) REVERT: A 900 MET cc_start: 0.9023 (ttp) cc_final: 0.8323 (tpt) REVERT: A 1146 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 1166 ARG cc_start: 0.4890 (ttp80) cc_final: 0.2256 (tpt170) outliers start: 22 outliers final: 13 residues processed: 116 average time/residue: 0.0687 time to fit residues: 11.8826 Evaluate side-chains 99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072307 restraints weight = 21425.309| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.37 r_work: 0.2975 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2122 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= 0.113 Angle : 0.498 7.841 10601 Z= 0.247 Chirality : 0.037 0.126 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.450 16.580 1072 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.97 % Allowed : 13.78 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.29), residues: 958 helix: 2.82 (0.21), residues: 599 sheet: -0.28 (0.69), residues: 65 loop : -0.82 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.018 0.001 TYR A1168 PHE 0.021 0.001 PHE A 902 TRP 0.010 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7703) covalent geometry : angle 0.49786 (10599) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.42046 ( 2) hydrogen bonds : bond 0.03599 ( 473) hydrogen bonds : angle 3.93537 ( 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 124 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.242 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 9 SER cc_start: 0.8784 (m) cc_final: 0.8409 (t) REVERT: A 186 MET cc_start: 0.9242 (mmm) cc_final: 0.8993 (mmp) REVERT: A 355 MET cc_start: 0.9612 (mmp) cc_final: 0.9392 (mmm) REVERT: A 608 GLU cc_start: 0.8763 (mp0) cc_final: 0.8437 (mp0) REVERT: A 818 TYR cc_start: 0.9017 (m-10) cc_final: 0.8795 (m-80) REVERT: A 827 GLU cc_start: 0.8935 (tp30) cc_final: 0.8563 (tp30) REVERT: A 884 THR cc_start: 0.8981 (m) cc_final: 0.8492 (p) REVERT: A 900 MET cc_start: 0.8960 (ttp) cc_final: 0.8242 (tpt) REVERT: A 1166 ARG cc_start: 0.5052 (ttp80) cc_final: 0.2377 (tpt170) outliers start: 22 outliers final: 15 residues processed: 118 average time/residue: 0.0681 time to fit residues: 11.7295 Evaluate side-chains 105 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 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 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 833 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 974 ILE 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: 9.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070180 restraints weight = 21473.794| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.32 r_work: 0.2924 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2329 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= 0.183 Angle : 0.546 8.408 10601 Z= 0.271 Chirality : 0.038 0.125 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.485 16.302 1072 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.11 % Allowed : 15.41 % 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 aren not related in a simple way. whole: 2.29 (0.29), residues: 958 helix: 2.82 (0.21), residues: 601 sheet: -0.32 (0.69), residues: 64 loop : -0.93 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.018 0.001 TYR A1168 PHE 0.011 0.001 PHE A 627 TRP 0.011 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7703) covalent geometry : angle 0.54557 (10599) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.64306 ( 2) hydrogen bonds : bond 0.03883 ( 473) hydrogen bonds : angle 4.02858 ( 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 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.297 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 430 MET cc_start: 0.9192 (mmm) cc_final: 0.8965 (tpp) REVERT: A 608 GLU cc_start: 0.8834 (mp0) cc_final: 0.8474 (mp0) REVERT: A 818 TYR cc_start: 0.9024 (m-10) cc_final: 0.8798 (m-80) REVERT: A 827 GLU cc_start: 0.9009 (tp30) cc_final: 0.8659 (tp30) REVERT: A 884 THR cc_start: 0.9006 (m) cc_final: 0.8271 (p) REVERT: A 900 MET cc_start: 0.8976 (ttp) cc_final: 0.8275 (tpt) REVERT: A 1166 ARG cc_start: 0.5033 (ttp80) cc_final: 0.2316 (tpt170) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.0676 time to fit residues: 10.4197 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 974 ILE Chi-restraints excluded: chain A residue 983 MET 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: 4.9990 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071169 restraints weight = 21308.588| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.34 r_work: 0.2942 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7704 Z= 0.134 Angle : 0.514 7.653 10601 Z= 0.255 Chirality : 0.037 0.124 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.449 16.026 1072 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.24 % Allowed : 15.68 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.29), residues: 958 helix: 2.83 (0.21), residues: 600 sheet: -0.28 (0.70), residues: 64 loop : -0.94 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.018 0.001 TYR A1168 PHE 0.009 0.001 PHE A 627 TRP 0.009 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7703) covalent geometry : angle 0.51439 (10599) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.53717 ( 2) hydrogen bonds : bond 0.03690 ( 473) hydrogen bonds : angle 3.94910 ( 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 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.200 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 355 MET cc_start: 0.9616 (mmp) cc_final: 0.9415 (mmm) REVERT: A 430 MET cc_start: 0.9204 (mmm) cc_final: 0.8980 (tpp) REVERT: A 440 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8244 (t80) REVERT: A 608 GLU cc_start: 0.8870 (mp0) cc_final: 0.8546 (mp0) REVERT: A 622 MET cc_start: 0.8717 (mtp) cc_final: 0.8501 (mtm) REVERT: A 644 ARG cc_start: 0.5858 (mmt180) cc_final: 0.5500 (tpt170) REVERT: A 818 TYR cc_start: 0.9013 (m-10) cc_final: 0.8792 (m-80) REVERT: A 827 GLU cc_start: 0.9000 (tp30) cc_final: 0.8612 (tp30) REVERT: A 884 THR cc_start: 0.8995 (m) cc_final: 0.8507 (p) REVERT: A 900 MET cc_start: 0.8967 (ttp) cc_final: 0.8270 (tpt) REVERT: A 1166 ARG cc_start: 0.5108 (ttp80) cc_final: 0.2391 (tpt170) outliers start: 24 outliers final: 14 residues processed: 107 average time/residue: 0.0650 time to fit residues: 10.2046 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 440 PHE 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 1023 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: 3.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.068537 restraints weight = 21537.664| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.29 r_work: 0.2890 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7704 Z= 0.242 Angle : 0.588 8.377 10601 Z= 0.293 Chirality : 0.039 0.132 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.543 15.053 1072 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.97 % Allowed : 16.89 % 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 aren not related in a simple way. whole: 2.19 (0.29), residues: 958 helix: 2.77 (0.21), residues: 601 sheet: -0.41 (0.70), residues: 63 loop : -1.02 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 771 TYR 0.018 0.001 TYR A1168 PHE 0.012 0.001 PHE A 627 TRP 0.010 0.001 TRP A 820 HIS 0.007 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 7703) covalent geometry : angle 0.58828 (10599) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.75984 ( 2) hydrogen bonds : bond 0.04121 ( 473) hydrogen bonds : angle 4.14361 ( 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 102 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.317 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 355 MET cc_start: 0.9643 (mmp) cc_final: 0.9443 (mmm) REVERT: A 430 MET cc_start: 0.9225 (mmm) cc_final: 0.8991 (tpp) REVERT: A 440 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8281 (t80) REVERT: A 608 GLU cc_start: 0.8926 (mp0) cc_final: 0.8565 (mp0) REVERT: A 644 ARG cc_start: 0.5899 (mmt180) cc_final: 0.5438 (tpt170) REVERT: A 818 TYR cc_start: 0.9054 (m-10) cc_final: 0.8834 (m-80) REVERT: A 827 GLU cc_start: 0.9069 (tp30) cc_final: 0.8715 (tp30) REVERT: A 900 MET cc_start: 0.9019 (ttp) cc_final: 0.8318 (tpt) REVERT: A 1166 ARG cc_start: 0.5362 (ttp80) cc_final: 0.2599 (tpt170) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.0602 time to fit residues: 9.1050 Evaluate side-chains 90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 440 PHE 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 974 ILE Chi-restraints excluded: chain A residue 1023 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: 6.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3401 r_free = 0.3401 target = 0.087475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.070552 restraints weight = 21530.144| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.35 r_work: 0.2935 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7704 Z= 0.128 Angle : 0.518 8.363 10601 Z= 0.256 Chirality : 0.037 0.157 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.469 14.057 1072 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.30 % Allowed : 17.70 % Favored : 80.00 % 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 aren not related in a simple way. whole: 2.21 (0.29), residues: 958 helix: 2.80 (0.21), residues: 600 sheet: -0.59 (0.68), residues: 64 loop : -0.99 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.019 0.001 TYR A1168 PHE 0.010 0.001 PHE A 373 TRP 0.012 0.001 TRP A 403 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7703) covalent geometry : angle 0.51847 (10599) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.57318 ( 2) hydrogen bonds : bond 0.03708 ( 473) hydrogen bonds : angle 3.96138 ( 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 106 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.224 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 355 MET cc_start: 0.9616 (mmp) cc_final: 0.9394 (mmm) REVERT: A 608 GLU cc_start: 0.8916 (mp0) cc_final: 0.8593 (mp0) REVERT: A 644 ARG cc_start: 0.5906 (mmt180) cc_final: 0.5438 (tpt170) REVERT: A 827 GLU cc_start: 0.9016 (tp30) cc_final: 0.8628 (tp30) REVERT: A 900 MET cc_start: 0.8967 (ttp) cc_final: 0.8263 (tpt) REVERT: A 1166 ARG cc_start: 0.5351 (ttp80) cc_final: 0.2573 (tpt170) outliers start: 17 outliers final: 17 residues processed: 104 average time/residue: 0.0601 time to fit residues: 9.1939 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 : 0.270 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 315 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 974 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1050 VAL 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: 0.9990 chunk 60 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.089147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072269 restraints weight = 21153.336| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.35 r_work: 0.2967 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7704 Z= 0.106 Angle : 0.508 8.170 10601 Z= 0.251 Chirality : 0.036 0.124 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.400 13.187 1072 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.70 % Allowed : 17.97 % Favored : 79.32 % 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 aren not related in a simple way. whole: 2.20 (0.29), residues: 958 helix: 2.80 (0.21), residues: 600 sheet: -0.63 (0.68), residues: 64 loop : -1.00 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.032 0.001 TYR A 818 PHE 0.009 0.001 PHE A 627 TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7703) covalent geometry : angle 0.50845 (10599) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.48012 ( 2) hydrogen bonds : bond 0.03489 ( 473) hydrogen bonds : angle 3.87491 ( 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 107 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.307 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 355 MET cc_start: 0.9605 (mmp) cc_final: 0.9387 (mmm) REVERT: A 440 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8160 (t80) REVERT: A 608 GLU cc_start: 0.8889 (mp0) cc_final: 0.8582 (mp0) REVERT: A 644 ARG cc_start: 0.5885 (mmt180) cc_final: 0.5401 (tpt170) REVERT: A 827 GLU cc_start: 0.8980 (tp30) cc_final: 0.8584 (tp30) REVERT: A 900 MET cc_start: 0.8952 (ttp) cc_final: 0.8197 (tpt) REVERT: A 1166 ARG cc_start: 0.5346 (ttp80) cc_final: 0.2570 (tpt170) outliers start: 20 outliers final: 16 residues processed: 103 average time/residue: 0.0680 time to fit residues: 10.3526 Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 440 PHE 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 824 LEU Chi-restraints excluded: chain A residue 1050 VAL 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: 0.0000 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.0060 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3448 r_free = 0.3448 target = 0.089807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073025 restraints weight = 21171.818| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.37 r_work: 0.2982 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2945 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= 0.101 Angle : 0.521 12.102 10601 Z= 0.255 Chirality : 0.038 0.374 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.368 13.272 1072 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.43 % Allowed : 19.19 % Favored : 78.38 % 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 aren not related in a simple way. whole: 2.17 (0.28), residues: 958 helix: 2.77 (0.21), residues: 600 sheet: -0.76 (0.67), residues: 65 loop : -0.98 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.019 0.001 TYR A1168 PHE 0.009 0.001 PHE A 902 TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7703) covalent geometry : angle 0.52082 (10599) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.43871 ( 2) hydrogen bonds : bond 0.03362 ( 473) hydrogen bonds : angle 3.84725 ( 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 111 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.274 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 430 MET cc_start: 0.9324 (mmm) cc_final: 0.8956 (tpp) REVERT: A 440 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 608 GLU cc_start: 0.8877 (mp0) cc_final: 0.8580 (mp0) REVERT: A 644 ARG cc_start: 0.5858 (mmt180) cc_final: 0.5349 (tpt170) REVERT: A 827 GLU cc_start: 0.8974 (tp30) cc_final: 0.8571 (tp30) REVERT: A 900 MET cc_start: 0.8914 (ttp) cc_final: 0.8122 (tpt) REVERT: A 1166 ARG cc_start: 0.5265 (ttp80) cc_final: 0.2540 (tpt170) outliers start: 18 outliers final: 17 residues processed: 108 average time/residue: 0.0745 time to fit residues: 11.7726 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 440 PHE 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 824 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1050 VAL 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 77 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3431 r_free = 0.3431 target = 0.088959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072072 restraints weight = 21160.580| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.37 r_work: 0.2971 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3001 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= 0.124 Angle : 0.529 8.621 10601 Z= 0.260 Chirality : 0.038 0.317 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.374 13.324 1072 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.70 % Allowed : 19.73 % Favored : 77.57 % 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 aren not related in a simple way. whole: 2.13 (0.28), residues: 958 helix: 2.74 (0.21), residues: 600 sheet: -0.68 (0.68), residues: 64 loop : -1.01 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00280 ( 7703) covalent geometry : angle 0.52919 (10599) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.48062 ( 2) hydrogen bonds : bond 0.03457 ( 473) hydrogen bonds : angle 3.90881 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.64 seconds wall clock time: 30 minutes 2.91 seconds (1802.91 seconds total)