Starting phenix.real_space_refine on Wed Feb 12 09:27:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.map" model { file = "/net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6y_31753/02_2025/7v6y_31753.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 4923 2.51 5 N 1221 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7326 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 44, 'TRANS': 945} Chain breaks: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 29, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Unusual residues: {'5VI': 1, 'CLR': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.20, per 1000 atoms: 0.69 Number of scatterers: 7484 At special positions: 0 Unit cell: (93.48, 86.92, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1301 8.00 N 1221 7.00 C 4923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1204 " - " ASN A 127 " " NAG A1206 " - " ASN A 400 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 982.1 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 64.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 61 through 83 removed outlier: 3.661A pdb=" N LEU A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.572A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TRP A 222 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A 223 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.587A pdb=" N PHE A 245 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 294 through 298 removed outlier: 4.141A pdb=" N ASN A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.612A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.754A pdb=" N GLY A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.786A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 397 removed outlier: 4.529A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 455 through 478 removed outlier: 3.768A pdb=" N LEU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 514 Proline residue: A 490 - end of helix removed outlier: 4.007A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 549 removed outlier: 3.624A pdb=" N GLU A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 575 Processing helix chain 'A' and resid 576 through 592 removed outlier: 4.071A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.544A pdb=" N ALA A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 756 removed outlier: 4.066A pdb=" N VAL A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.931A pdb=" N HIS A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 810 " --> pdb=" O TYR A 806 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 852 Processing helix chain 'A' and resid 865 through 875 removed outlier: 3.594A pdb=" N GLN A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.795A pdb=" N TYR A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 991 removed outlier: 3.573A pdb=" N LEU A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.512A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1034 Processing helix chain 'A' and resid 1035 through 1061 Processing helix chain 'A' and resid 1065 through 1093 removed outlier: 4.566A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1127 removed outlier: 3.747A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Proline residue: A1111 - end of helix Processing helix chain 'A' and resid 1131 through 1164 removed outlier: 3.547A pdb=" N VAL A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A1139 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.538A pdb=" N CYS A 313 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 4.043A pdb=" N SER A 342 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA5, first strand: chain 'A' and resid 963 through 965 465 hydrogen bonds defined for protein. 1362 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: 2.33 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1135 1.28 - 1.41: 2003 1.41 - 1.54: 4444 1.54 - 1.68: 32 1.68 - 1.81: 60 Bond restraints: 7674 Sorted by residual: bond pdb=" C LEU A1145 " pdb=" O LEU A1145 " ideal model delta sigma weight residual 1.237 1.146 0.090 1.17e-02 7.31e+03 5.98e+01 bond pdb=" CA HIS A 164 " pdb=" C HIS A 164 " ideal model delta sigma weight residual 1.523 1.425 0.099 1.30e-02 5.92e+03 5.77e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.92e+01 bond pdb=" CA GLN A 228 " pdb=" C GLN A 228 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.24e-02 6.50e+03 4.92e+01 bond pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.31e+01 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9410 2.78 - 5.55: 889 5.55 - 8.33: 144 8.33 - 11.10: 56 11.10 - 13.88: 13 Bond angle restraints: 10512 Sorted by residual: angle pdb=" N THR A 293 " pdb=" CA THR A 293 " pdb=" C THR A 293 " ideal model delta sigma weight residual 113.17 99.29 13.88 1.26e+00 6.30e-01 1.21e+02 angle pdb=" N LYS A 339 " pdb=" CA LYS A 339 " pdb=" C LYS A 339 " ideal model delta sigma weight residual 111.28 122.74 -11.46 1.09e+00 8.42e-01 1.10e+02 angle pdb=" N GLN A 794 " pdb=" CA GLN A 794 " pdb=" C GLN A 794 " ideal model delta sigma weight residual 111.14 122.39 -11.25 1.08e+00 8.57e-01 1.09e+02 angle pdb=" N THR A 764 " pdb=" CA THR A 764 " pdb=" C THR A 764 " ideal model delta sigma weight residual 113.23 101.13 12.10 1.24e+00 6.50e-01 9.53e+01 angle pdb=" N ILE A 328 " pdb=" CA ILE A 328 " pdb=" C ILE A 328 " ideal model delta sigma weight residual 111.67 120.48 -8.81 9.50e-01 1.11e+00 8.61e+01 ... (remaining 10507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4070 16.95 - 33.90: 380 33.90 - 50.86: 138 50.86 - 67.81: 46 67.81 - 84.76: 11 Dihedral angle restraints: 4645 sinusoidal: 1758 harmonic: 2887 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual 93.00 171.16 -78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" C PHE A1131 " pdb=" N PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual -122.60 -138.95 16.35 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual 122.80 138.50 -15.70 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 4642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 977 0.139 - 0.278: 234 0.278 - 0.418: 39 0.418 - 0.557: 11 0.557 - 0.696: 4 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA PHE A 743 " pdb=" N PHE A 743 " pdb=" C PHE A 743 " pdb=" CB PHE A 743 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE A1131 " pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CB PHE A1131 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP A 183 " pdb=" N TRP A 183 " pdb=" C TRP A 183 " pdb=" CB TRP A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.50e+00 ... (remaining 1262 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.199 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" C7 NAG B 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.086 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A1158 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 361 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C HIS A 361 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS A 361 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE A 362 " 0.030 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2189 2.79 - 3.31: 7486 3.31 - 3.84: 12182 3.84 - 4.37: 14405 4.37 - 4.90: 23391 Nonbonded interactions: 59653 Sorted by model distance: nonbonded pdb=" OE2 GLU A 108 " pdb=" CB SER A 480 " model vdw 2.258 3.440 nonbonded pdb=" O SER A 401 " pdb=" OG1 THR A 402 " model vdw 2.269 3.040 nonbonded pdb=" N THR A 293 " pdb=" N ALA A 294 " model vdw 2.281 2.560 nonbonded pdb=" O PHE A 545 " pdb=" OG SER A 560 " model vdw 2.339 3.040 nonbonded pdb=" N MET A 178 " pdb=" O MET A 178 " model vdw 2.342 2.496 ... (remaining 59648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.010 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.014 0.099 7674 Z= 0.927 Angle : 1.855 13.878 10512 Z= 1.262 Chirality : 0.132 0.696 1265 Planarity : 0.012 0.164 1295 Dihedral : 16.465 84.758 2776 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.51 % Rotamer: Outliers : 11.06 % Allowed : 11.91 % Favored : 77.02 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 984 helix: 1.40 (0.21), residues: 589 sheet: 0.32 (0.72), residues: 49 loop : -1.38 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 830 HIS 0.004 0.001 HIS A 164 PHE 0.034 0.003 PHE A1133 TYR 0.028 0.003 TYR A 920 ARG 0.006 0.001 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.758 Fit side-chains REVERT: A 115 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.5166 (t60) REVERT: A 182 GLN cc_start: 0.7559 (tp40) cc_final: 0.7109 (tp-100) REVERT: A 259 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6682 (t80) REVERT: A 264 TRP cc_start: 0.6988 (m-90) cc_final: 0.6529 (m-90) REVERT: A 349 MET cc_start: 0.7665 (mtt) cc_final: 0.7412 (mtt) REVERT: A 358 MET cc_start: 0.8183 (ttt) cc_final: 0.7899 (ttt) REVERT: A 367 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.6058 (t80) REVERT: A 444 LEU cc_start: 0.7921 (tp) cc_final: 0.7612 (mp) REVERT: A 479 ILE cc_start: 0.9160 (mt) cc_final: 0.8951 (mt) REVERT: A 588 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.6669 (mmt-90) REVERT: A 794 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: A 1134 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7654 (mp) outliers start: 78 outliers final: 20 residues processed: 226 average time/residue: 0.1945 time to fit residues: 60.1231 Evaluate side-chains 149 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 182 GLN A 244 ASN A 269 ASN A 284 ASN A 296 ASN A 351 GLN A 506 HIS A 570 ASN A 780 GLN A 800 ASN A 809 HIS A 891 GLN A 985 ASN A1085 HIS ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.224441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.178891 restraints weight = 7398.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.181225 restraints weight = 6562.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.183937 restraints weight = 4390.015| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7674 Z= 0.246 Angle : 0.717 9.168 10512 Z= 0.368 Chirality : 0.044 0.180 1265 Planarity : 0.006 0.072 1295 Dihedral : 10.802 58.771 1373 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.24 % Allowed : 16.74 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 984 helix: 1.28 (0.20), residues: 606 sheet: 0.24 (0.72), residues: 48 loop : -1.48 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 373 HIS 0.006 0.001 HIS A 322 PHE 0.035 0.002 PHE A1133 TYR 0.022 0.002 TYR A 190 ARG 0.006 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.830 Fit side-chains REVERT: A 259 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5579 (t80) REVERT: A 349 MET cc_start: 0.7622 (mtt) cc_final: 0.7394 (mtt) REVERT: A 373 TRP cc_start: 0.6266 (t-100) cc_final: 0.5978 (t-100) REVERT: A 479 ILE cc_start: 0.9151 (mt) cc_final: 0.8892 (mt) REVERT: A 519 PHE cc_start: 0.7433 (t80) cc_final: 0.7081 (t80) REVERT: A 588 ARG cc_start: 0.7598 (tmm-80) cc_final: 0.6942 (mpt180) REVERT: A 797 ASP cc_start: 0.7458 (p0) cc_final: 0.7088 (p0) REVERT: A 949 ILE cc_start: 0.7253 (mm) cc_final: 0.6967 (mm) REVERT: A 1015 LEU cc_start: 0.7429 (tp) cc_final: 0.7217 (tp) REVERT: A 1134 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (mp) outliers start: 44 outliers final: 24 residues processed: 166 average time/residue: 0.1743 time to fit residues: 40.2796 Evaluate side-chains 138 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 403 GLN A 506 HIS A 901 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.225966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184350 restraints weight = 7644.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182983 restraints weight = 10050.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.186242 restraints weight = 7426.919| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7674 Z= 0.223 Angle : 0.623 7.306 10512 Z= 0.324 Chirality : 0.042 0.176 1265 Planarity : 0.006 0.052 1295 Dihedral : 8.712 58.466 1344 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.67 % Allowed : 18.44 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 984 helix: 1.38 (0.20), residues: 599 sheet: 0.21 (0.71), residues: 48 loop : -1.44 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 115 HIS 0.005 0.001 HIS A 164 PHE 0.030 0.002 PHE A1133 TYR 0.029 0.001 TYR A 190 ARG 0.005 0.000 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.816 Fit side-chains REVERT: A 259 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5070 (t80) REVERT: A 349 MET cc_start: 0.7940 (mtt) cc_final: 0.7689 (mtt) REVERT: A 479 ILE cc_start: 0.9209 (mt) cc_final: 0.8933 (mt) REVERT: A 588 ARG cc_start: 0.7605 (tmm-80) cc_final: 0.6787 (mmt-90) REVERT: A 797 ASP cc_start: 0.7361 (p0) cc_final: 0.7016 (p0) REVERT: A 901 ASN cc_start: 0.8408 (t0) cc_final: 0.8151 (t0) REVERT: A 949 ILE cc_start: 0.7351 (mm) cc_final: 0.7143 (mm) REVERT: A 1134 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7693 (mp) outliers start: 40 outliers final: 28 residues processed: 159 average time/residue: 0.1814 time to fit residues: 39.9737 Evaluate side-chains 144 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 chunk 59 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.227940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183967 restraints weight = 7542.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.184848 restraints weight = 7258.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188360 restraints weight = 5188.463| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7674 Z= 0.186 Angle : 0.599 8.348 10512 Z= 0.304 Chirality : 0.041 0.169 1265 Planarity : 0.005 0.051 1295 Dihedral : 7.943 57.158 1344 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.67 % Allowed : 20.43 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 984 helix: 1.53 (0.21), residues: 598 sheet: 0.16 (0.72), residues: 48 loop : -1.41 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.006 0.001 HIS A 164 PHE 0.025 0.002 PHE A1133 TYR 0.025 0.001 TYR A 190 ARG 0.005 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7873 (t80) cc_final: 0.7597 (t80) REVERT: A 231 THR cc_start: 0.8649 (t) cc_final: 0.8391 (p) REVERT: A 259 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.4845 (t80) REVERT: A 349 MET cc_start: 0.7885 (mtt) cc_final: 0.7619 (mtt) REVERT: A 450 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7833 (ptpp) REVERT: A 479 ILE cc_start: 0.9210 (mt) cc_final: 0.8941 (mt) REVERT: A 588 ARG cc_start: 0.7513 (tmm-80) cc_final: 0.6765 (mpt180) REVERT: A 797 ASP cc_start: 0.7251 (p0) cc_final: 0.6949 (p0) outliers start: 40 outliers final: 33 residues processed: 160 average time/residue: 0.1722 time to fit residues: 38.9470 Evaluate side-chains 151 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.222829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179336 restraints weight = 7521.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178146 restraints weight = 8374.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.182095 restraints weight = 6461.944| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7674 Z= 0.194 Angle : 0.594 8.900 10512 Z= 0.300 Chirality : 0.041 0.194 1265 Planarity : 0.005 0.056 1295 Dihedral : 7.375 56.060 1344 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.25 % Allowed : 22.55 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 984 helix: 1.54 (0.20), residues: 602 sheet: 0.25 (0.76), residues: 48 loop : -1.42 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS A 164 PHE 0.023 0.001 PHE A1133 TYR 0.019 0.001 TYR A 190 ARG 0.011 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7658 (t80) cc_final: 0.7358 (t80) REVERT: A 231 THR cc_start: 0.8597 (t) cc_final: 0.8374 (p) REVERT: A 259 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.4671 (t80) REVERT: A 314 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: A 349 MET cc_start: 0.8102 (mtt) cc_final: 0.7791 (mtp) REVERT: A 403 GLN cc_start: 0.6979 (mm110) cc_final: 0.6722 (mm110) REVERT: A 479 ILE cc_start: 0.9183 (mt) cc_final: 0.8922 (mt) REVERT: A 588 ARG cc_start: 0.7597 (tmm-80) cc_final: 0.6896 (mpt180) REVERT: A 797 ASP cc_start: 0.7193 (p0) cc_final: 0.6913 (p0) outliers start: 37 outliers final: 25 residues processed: 145 average time/residue: 0.1685 time to fit residues: 34.4225 Evaluate side-chains 138 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.225333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.181746 restraints weight = 7636.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180937 restraints weight = 8164.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184922 restraints weight = 6314.861| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.197 Angle : 0.593 8.589 10512 Z= 0.299 Chirality : 0.041 0.181 1265 Planarity : 0.005 0.056 1295 Dihedral : 7.110 57.916 1343 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.96 % Allowed : 23.12 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 984 helix: 1.54 (0.20), residues: 602 sheet: 0.13 (0.78), residues: 48 loop : -1.43 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS A 164 PHE 0.021 0.001 PHE A1133 TYR 0.027 0.001 TYR A 190 ARG 0.004 0.000 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7663 (t80) cc_final: 0.7298 (t80) REVERT: A 216 THR cc_start: 0.8396 (p) cc_final: 0.8165 (p) REVERT: A 259 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.4661 (t80) REVERT: A 349 MET cc_start: 0.8088 (mtt) cc_final: 0.7786 (mtp) REVERT: A 479 ILE cc_start: 0.9204 (mt) cc_final: 0.8961 (mt) REVERT: A 588 ARG cc_start: 0.7609 (tmm-80) cc_final: 0.6932 (mpt180) REVERT: A 797 ASP cc_start: 0.7177 (p0) cc_final: 0.6934 (p0) outliers start: 35 outliers final: 28 residues processed: 142 average time/residue: 0.1816 time to fit residues: 36.3479 Evaluate side-chains 139 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.224854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.182355 restraints weight = 7398.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.181185 restraints weight = 8033.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186331 restraints weight = 6022.522| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.175 Angle : 0.587 11.929 10512 Z= 0.293 Chirality : 0.040 0.160 1265 Planarity : 0.005 0.057 1295 Dihedral : 6.777 59.422 1341 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.39 % Allowed : 22.84 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 984 helix: 1.62 (0.20), residues: 606 sheet: 0.16 (0.80), residues: 48 loop : -1.44 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS A 164 PHE 0.025 0.001 PHE A 786 TYR 0.026 0.001 TYR A 190 ARG 0.004 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7616 (t80) cc_final: 0.7304 (t80) REVERT: A 259 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.4551 (t80) REVERT: A 349 MET cc_start: 0.8072 (mtt) cc_final: 0.7768 (mtp) REVERT: A 479 ILE cc_start: 0.9181 (mt) cc_final: 0.8952 (mt) REVERT: A 585 ASP cc_start: 0.7784 (t0) cc_final: 0.7394 (t0) REVERT: A 588 ARG cc_start: 0.7593 (tmm-80) cc_final: 0.6935 (mpt180) outliers start: 38 outliers final: 25 residues processed: 147 average time/residue: 0.1736 time to fit residues: 36.2492 Evaluate side-chains 129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 322 HIS A 562 GLN A 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.218431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174960 restraints weight = 7594.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173054 restraints weight = 8368.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177704 restraints weight = 6088.353| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7674 Z= 0.272 Angle : 0.639 11.437 10512 Z= 0.324 Chirality : 0.042 0.184 1265 Planarity : 0.005 0.056 1295 Dihedral : 6.912 57.756 1341 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.54 % Allowed : 24.54 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 984 helix: 1.50 (0.20), residues: 603 sheet: -0.08 (0.79), residues: 48 loop : -1.37 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 373 HIS 0.002 0.001 HIS A 164 PHE 0.028 0.002 PHE A1133 TYR 0.027 0.002 TYR A 190 ARG 0.012 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7654 (t80) cc_final: 0.7288 (t80) REVERT: A 259 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.4473 (t80) REVERT: A 349 MET cc_start: 0.8067 (mtt) cc_final: 0.7756 (mtp) REVERT: A 450 LYS cc_start: 0.8026 (mttm) cc_final: 0.7730 (ptpp) REVERT: A 479 ILE cc_start: 0.9188 (mt) cc_final: 0.8965 (mt) REVERT: A 547 MET cc_start: 0.7189 (tpp) cc_final: 0.6901 (mmt) REVERT: A 585 ASP cc_start: 0.7826 (t0) cc_final: 0.7428 (t0) REVERT: A 588 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.6969 (mpt180) REVERT: A 1134 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7751 (mt) outliers start: 32 outliers final: 22 residues processed: 138 average time/residue: 0.1745 time to fit residues: 33.9040 Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.223711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.180573 restraints weight = 7603.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180238 restraints weight = 8308.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.184509 restraints weight = 5802.415| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.179 Angle : 0.598 12.215 10512 Z= 0.298 Chirality : 0.040 0.164 1265 Planarity : 0.005 0.057 1295 Dihedral : 6.682 59.416 1340 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.97 % Allowed : 24.96 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 984 helix: 1.59 (0.21), residues: 605 sheet: 0.03 (0.81), residues: 48 loop : -1.39 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 373 HIS 0.004 0.001 HIS A 164 PHE 0.025 0.002 PHE A 786 TYR 0.026 0.001 TYR A 190 ARG 0.014 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7655 (t80) cc_final: 0.7314 (t80) REVERT: A 259 TYR cc_start: 0.5717 (OUTLIER) cc_final: 0.4335 (t80) REVERT: A 349 MET cc_start: 0.8095 (mtt) cc_final: 0.7778 (mtp) REVERT: A 479 ILE cc_start: 0.9250 (mt) cc_final: 0.9012 (mt) REVERT: A 547 MET cc_start: 0.7373 (tpp) cc_final: 0.6867 (mmt) REVERT: A 585 ASP cc_start: 0.7843 (t0) cc_final: 0.7429 (t0) REVERT: A 588 ARG cc_start: 0.7650 (tmm-80) cc_final: 0.6839 (mpt180) REVERT: A 1134 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7730 (mt) outliers start: 28 outliers final: 21 residues processed: 133 average time/residue: 0.1773 time to fit residues: 33.1775 Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.223915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179153 restraints weight = 7535.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177353 restraints weight = 8214.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182077 restraints weight = 6037.098| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7674 Z= 0.230 Angle : 0.629 12.038 10512 Z= 0.312 Chirality : 0.041 0.164 1265 Planarity : 0.005 0.057 1295 Dihedral : 6.771 59.987 1340 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.55 % Allowed : 25.53 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 984 helix: 1.55 (0.20), residues: 608 sheet: -0.08 (0.81), residues: 48 loop : -1.39 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 373 HIS 0.003 0.001 HIS A 164 PHE 0.024 0.001 PHE A1133 TYR 0.025 0.001 TYR A 190 ARG 0.013 0.001 ARG A 892 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7610 (t80) cc_final: 0.7301 (t80) REVERT: A 259 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4205 (t80) REVERT: A 349 MET cc_start: 0.8064 (mtt) cc_final: 0.7748 (mtp) REVERT: A 479 ILE cc_start: 0.9232 (mt) cc_final: 0.9011 (mt) REVERT: A 573 MET cc_start: 0.8248 (tmm) cc_final: 0.7845 (tmm) REVERT: A 585 ASP cc_start: 0.7835 (t0) cc_final: 0.7335 (t0) REVERT: A 588 ARG cc_start: 0.7692 (tmm-80) cc_final: 0.6943 (mpt180) REVERT: A 1134 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7798 (mt) outliers start: 25 outliers final: 21 residues processed: 131 average time/residue: 0.1781 time to fit residues: 33.0153 Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.225654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.181758 restraints weight = 7517.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180071 restraints weight = 8796.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185391 restraints weight = 6537.394| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.200 Angle : 0.615 11.584 10512 Z= 0.307 Chirality : 0.040 0.163 1265 Planarity : 0.005 0.057 1295 Dihedral : 6.658 59.588 1340 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.69 % Allowed : 25.67 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 984 helix: 1.65 (0.21), residues: 603 sheet: -0.04 (0.82), residues: 48 loop : -1.38 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 373 HIS 0.003 0.001 HIS A 164 PHE 0.025 0.001 PHE A 786 TYR 0.025 0.001 TYR A 190 ARG 0.013 0.001 ARG A 892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.64 seconds wall clock time: 43 minutes 42.34 seconds (2622.34 seconds total)