Starting phenix.real_space_refine on Tue Feb 13 19:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_31753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_31753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_31753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_31753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/02_2024/7v6y_31753_updated.pdb" } 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 Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.89, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 38 helices and 3 sheets defined 57.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.662A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 217 through 220 removed outlier: 3.572A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.786A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 396 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) Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 456 through 477 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 483 through 513 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 522 through 548 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 554 through 574 Processing helix chain 'A' and resid 577 through 591 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 719 through 731 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 733 through 755 removed outlier: 4.066A pdb=" N VAL A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 803 through 814 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) Processing helix chain 'A' and resid 830 through 851 Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.573A pdb=" N LEU A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.512A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU A1005 " --> pdb=" O PHE A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1000 through 1005' Processing helix chain 'A' and resid 1010 through 1033 Processing helix chain 'A' and resid 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1092 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 1097 through 1128 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 removed outlier: 4.557A pdb=" N GLY A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1163 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= A, first strand: chain 'A' and resid 345 through 352 Processing sheet with id= B, first strand: chain 'A' and resid 786 through 788 Processing sheet with id= C, first strand: chain 'A' and resid 789 through 793 404 hydrogen bonds defined for protein. 1206 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: 2.14 Time building geometry restraints manager: 3.64 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: 97.88 - 105.67: 269 105.67 - 113.45: 4059 113.45 - 121.24: 4682 121.24 - 129.03: 1426 129.03 - 136.82: 76 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: 2192 2.79 - 3.31: 7534 3.31 - 3.84: 12243 3.84 - 4.37: 14514 4.37 - 4.90: 23414 Nonbonded interactions: 59897 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 2.440 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 2.440 nonbonded pdb=" N MET A 178 " pdb=" O MET A 178 " model vdw 2.342 2.496 ... (remaining 59892 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 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: 0.920 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: 4.290 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- 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= 0.931 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 fitting. rotamer outliers: 78 poor density : 172 time to evaluate : 0.814 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: 0.1898 time to fit residues: 57.8040 Evaluate side-chains 149 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 146 GLN A 182 GLN A 244 ASN A 269 ASN A 284 ASN A 322 HIS A 351 GLN A 452 GLN A 506 HIS A 570 ASN A 780 GLN A 800 ASN A 809 HIS A 891 GLN A 901 ASN A 985 ASN A1085 HIS ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7674 Z= 0.232 Angle : 0.692 7.390 10512 Z= 0.355 Chirality : 0.044 0.173 1265 Planarity : 0.006 0.074 1295 Dihedral : 10.804 59.379 1373 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.52 % Allowed : 16.74 % Favored : 76.74 % 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: 0.54 (0.26), residues: 984 helix: 1.36 (0.21), residues: 595 sheet: 0.44 (0.74), residues: 48 loop : -1.49 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 373 HIS 0.007 0.001 HIS A 322 PHE 0.034 0.002 PHE A1133 TYR 0.024 0.002 TYR A 190 ARG 0.005 0.001 ARG A 892 *********************** 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 183 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 0.863 Fit side-chains REVERT: A 144 MET cc_start: 0.7458 (ttp) cc_final: 0.7242 (ttp) REVERT: A 259 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6183 (t80) REVERT: A 349 MET cc_start: 0.7666 (mtt) cc_final: 0.7413 (mtt) REVERT: A 363 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6940 (tpp80) REVERT: A 443 MET cc_start: 0.7959 (mtm) cc_final: 0.7740 (mtp) REVERT: A 444 LEU cc_start: 0.7901 (tp) cc_final: 0.7627 (mp) REVERT: A 479 ILE cc_start: 0.9220 (mt) cc_final: 0.8928 (mt) REVERT: A 519 PHE cc_start: 0.5480 (t80) cc_final: 0.5273 (t80) REVERT: A 588 ARG cc_start: 0.7614 (tmm-80) cc_final: 0.6253 (mmt-90) REVERT: A 901 ASN cc_start: 0.8240 (t0) cc_final: 0.7977 (t0) REVERT: A 949 ILE cc_start: 0.7416 (mm) cc_final: 0.7138 (mm) REVERT: A 1134 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7522 (mp) outliers start: 46 outliers final: 28 residues processed: 171 average time/residue: 0.1688 time to fit residues: 40.6697 Evaluate side-chains 152 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 167 SER 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 340 LEU Chi-restraints excluded: chain A residue 363 ARG 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 744 LEU 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 Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 30 optimal weight: 0.0370 chunk 72 optimal weight: 0.2980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 275 HIS A 403 GLN A 506 HIS A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7674 Z= 0.178 Angle : 0.592 7.247 10512 Z= 0.302 Chirality : 0.040 0.173 1265 Planarity : 0.005 0.051 1295 Dihedral : 8.534 58.550 1346 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.11 % Allowed : 19.15 % Favored : 75.74 % 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: 0.76 (0.26), residues: 984 helix: 1.52 (0.21), residues: 596 sheet: 0.29 (0.73), residues: 48 loop : -1.30 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.003 0.001 HIS A 164 PHE 0.026 0.002 PHE A1133 TYR 0.032 0.001 TYR A 190 ARG 0.003 0.000 ARG A1136 *********************** 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 171 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 0.843 Fit side-chains REVERT: A 259 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5879 (t80) REVERT: A 349 MET cc_start: 0.7849 (mtt) cc_final: 0.7570 (mtt) REVERT: A 444 LEU cc_start: 0.8081 (tp) cc_final: 0.7863 (mp) REVERT: A 479 ILE cc_start: 0.9242 (mt) cc_final: 0.8936 (mt) REVERT: A 588 ARG cc_start: 0.7625 (tmm-80) cc_final: 0.6297 (mmt-90) REVERT: A 797 ASP cc_start: 0.7692 (p0) cc_final: 0.7015 (p0) REVERT: A 901 ASN cc_start: 0.8278 (t0) cc_final: 0.8059 (t0) outliers start: 36 outliers final: 26 residues processed: 166 average time/residue: 0.1835 time to fit residues: 42.1909 Evaluate side-chains 149 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 308 VAL Chi-restraints excluded: chain A residue 314 GLN 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 440 CYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 530 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 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1033 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7674 Z= 0.190 Angle : 0.582 7.663 10512 Z= 0.292 Chirality : 0.040 0.172 1265 Planarity : 0.005 0.049 1295 Dihedral : 7.912 59.482 1344 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.38 % Allowed : 20.28 % Favored : 73.33 % 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: 0.79 (0.26), residues: 984 helix: 1.58 (0.21), residues: 594 sheet: 0.33 (0.76), residues: 48 loop : -1.38 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.002 0.001 HIS A 936 PHE 0.024 0.002 PHE A1133 TYR 0.021 0.001 TYR A 190 ARG 0.010 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 169 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 124 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8941 (mt) cc_final: 0.8677 (mt) REVERT: A 259 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.5590 (t80) REVERT: A 349 MET cc_start: 0.7870 (mtt) cc_final: 0.7551 (mtp) REVERT: A 444 LEU cc_start: 0.8059 (tp) cc_final: 0.7846 (mp) REVERT: A 479 ILE cc_start: 0.9250 (mt) cc_final: 0.8973 (mt) REVERT: A 588 ARG cc_start: 0.7665 (tmm-80) cc_final: 0.6523 (mpt180) REVERT: A 797 ASP cc_start: 0.7554 (p0) cc_final: 0.6943 (p0) REVERT: A 901 ASN cc_start: 0.8413 (t0) cc_final: 0.8142 (t0) outliers start: 45 outliers final: 28 residues processed: 160 average time/residue: 0.1701 time to fit residues: 38.2232 Evaluate side-chains 148 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 114 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 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 455 VAL Chi-restraints excluded: chain A residue 482 ASN 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 867 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1108 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 403 GLN A 562 GLN A 794 GLN A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7674 Z= 0.387 Angle : 0.707 9.416 10512 Z= 0.362 Chirality : 0.046 0.197 1265 Planarity : 0.006 0.049 1295 Dihedral : 8.118 59.236 1343 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.24 % Allowed : 22.27 % Favored : 71.49 % 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: 0.15 (0.26), residues: 984 helix: 1.05 (0.20), residues: 592 sheet: -0.09 (0.76), residues: 48 loop : -1.54 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 183 HIS 0.003 0.001 HIS A 930 PHE 0.032 0.002 PHE A1133 TYR 0.017 0.002 TYR A 190 ARG 0.003 0.001 ARG A 557 *********************** 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 172 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 0.870 Fit side-chains REVERT: A 156 LEU cc_start: 0.9008 (mt) cc_final: 0.8779 (mt) REVERT: A 259 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.5680 (t80) REVERT: A 270 LYS cc_start: 0.9222 (mtpp) cc_final: 0.8953 (mtpt) REVERT: A 277 TYR cc_start: 0.8141 (m-80) cc_final: 0.7916 (m-80) REVERT: A 314 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 349 MET cc_start: 0.7924 (mtt) cc_final: 0.7661 (mtt) REVERT: A 356 LYS cc_start: 0.8288 (tmtt) cc_final: 0.8073 (tptp) REVERT: A 394 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7451 (t-90) REVERT: A 479 ILE cc_start: 0.9278 (mt) cc_final: 0.9030 (mt) REVERT: A 588 ARG cc_start: 0.7686 (tmm-80) cc_final: 0.6559 (mpt180) REVERT: A 797 ASP cc_start: 0.8108 (p0) cc_final: 0.7393 (p0) REVERT: A 871 LYS cc_start: 0.8929 (mttt) cc_final: 0.8676 (mttt) REVERT: A 901 ASN cc_start: 0.8382 (t0) cc_final: 0.8150 (t0) REVERT: A 949 ILE cc_start: 0.6861 (mm) cc_final: 0.6608 (mm) REVERT: A 1134 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7489 (mt) outliers start: 44 outliers final: 28 residues processed: 164 average time/residue: 0.1662 time to fit residues: 38.6274 Evaluate side-chains 152 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 167 SER Chi-restraints excluded: chain A residue 259 TYR 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 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1080 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7674 Z= 0.255 Angle : 0.614 9.289 10512 Z= 0.310 Chirality : 0.041 0.174 1265 Planarity : 0.005 0.055 1295 Dihedral : 7.535 56.597 1341 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.53 % Allowed : 24.26 % Favored : 70.21 % 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: 0.38 (0.26), residues: 984 helix: 1.25 (0.21), residues: 595 sheet: -0.14 (0.81), residues: 48 loop : -1.47 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS A1085 PHE 0.028 0.002 PHE A1133 TYR 0.020 0.001 TYR A 190 ARG 0.011 0.001 ARG A 892 *********************** 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 163 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 0.836 Fit side-chains REVERT: A 156 LEU cc_start: 0.9003 (mt) cc_final: 0.8776 (mt) REVERT: A 259 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.5646 (t80) REVERT: A 270 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8965 (mtpt) REVERT: A 314 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: A 349 MET cc_start: 0.7952 (mtt) cc_final: 0.7671 (mtt) REVERT: A 394 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: A 479 ILE cc_start: 0.9291 (mt) cc_final: 0.9039 (mt) REVERT: A 547 MET cc_start: 0.7472 (tpp) cc_final: 0.6888 (mmt) REVERT: A 588 ARG cc_start: 0.7658 (tmm-80) cc_final: 0.6488 (mpt180) REVERT: A 797 ASP cc_start: 0.8094 (p0) cc_final: 0.7499 (p0) REVERT: A 901 ASN cc_start: 0.8486 (t0) cc_final: 0.8203 (t0) REVERT: A 978 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 1134 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7588 (mt) outliers start: 39 outliers final: 28 residues processed: 158 average time/residue: 0.1656 time to fit residues: 37.4570 Evaluate side-chains 152 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 167 SER 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 321 MET 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 444 LEU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1033 LEU 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 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7674 Z= 0.380 Angle : 0.685 11.609 10512 Z= 0.347 Chirality : 0.044 0.168 1265 Planarity : 0.005 0.054 1295 Dihedral : 7.784 59.029 1341 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.82 % Allowed : 23.12 % Favored : 71.06 % 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: 0.11 (0.26), residues: 984 helix: 1.05 (0.21), residues: 595 sheet: -0.49 (0.81), residues: 48 loop : -1.58 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 183 HIS 0.003 0.001 HIS A 930 PHE 0.032 0.002 PHE A1133 TYR 0.025 0.002 TYR A 190 ARG 0.011 0.001 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 161 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 0.829 Fit side-chains REVERT: A 156 LEU cc_start: 0.9031 (mt) cc_final: 0.8827 (mt) REVERT: A 259 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5540 (t80) REVERT: A 270 LYS cc_start: 0.9254 (mtpp) cc_final: 0.8982 (mtpt) REVERT: A 314 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7767 (pt0) REVERT: A 349 MET cc_start: 0.7938 (mtt) cc_final: 0.7680 (mtt) REVERT: A 394 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: A 479 ILE cc_start: 0.9293 (mt) cc_final: 0.9039 (mt) REVERT: A 588 ARG cc_start: 0.7677 (tmm-80) cc_final: 0.6462 (mpt180) REVERT: A 797 ASP cc_start: 0.8241 (p0) cc_final: 0.7613 (p0) REVERT: A 901 ASN cc_start: 0.8496 (t0) cc_final: 0.8225 (t0) REVERT: A 949 ILE cc_start: 0.6685 (mm) cc_final: 0.6394 (mm) REVERT: A 978 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 1134 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7645 (mt) outliers start: 41 outliers final: 29 residues processed: 155 average time/residue: 0.1479 time to fit residues: 33.2875 Evaluate side-chains 145 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 321 MET 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 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR 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 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 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 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 269 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4992 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= 0.201 Angle : 0.600 9.323 10512 Z= 0.300 Chirality : 0.040 0.167 1265 Planarity : 0.005 0.057 1295 Dihedral : 7.273 58.080 1341 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.96 % Allowed : 24.40 % Favored : 70.64 % 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: 0.46 (0.26), residues: 984 helix: 1.38 (0.21), residues: 590 sheet: -0.40 (0.81), residues: 48 loop : -1.49 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 242 HIS 0.002 0.001 HIS A1085 PHE 0.022 0.001 PHE A 408 TYR 0.021 0.001 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 153 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 190 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7427 (p90) REVERT: A 259 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5503 (t80) REVERT: A 270 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8904 (mtpt) REVERT: A 314 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: A 349 MET cc_start: 0.7949 (mtt) cc_final: 0.7679 (mtt) REVERT: A 479 ILE cc_start: 0.9272 (mt) cc_final: 0.9031 (mt) REVERT: A 547 MET cc_start: 0.7490 (tpp) cc_final: 0.6840 (mmp) REVERT: A 588 ARG cc_start: 0.7680 (tmm-80) cc_final: 0.6470 (mpt180) REVERT: A 797 ASP cc_start: 0.8109 (p0) cc_final: 0.7530 (p0) REVERT: A 901 ASN cc_start: 0.8488 (t0) cc_final: 0.8245 (t0) REVERT: A 949 ILE cc_start: 0.6486 (mm) cc_final: 0.6227 (mm) REVERT: A 978 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7690 (mt-10) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 0.1652 time to fit residues: 34.4042 Evaluate side-chains 139 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 440 CYS 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 546 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE 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 88 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 chunk 27 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5139 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= 0.198 Angle : 0.599 9.388 10512 Z= 0.300 Chirality : 0.040 0.188 1265 Planarity : 0.005 0.058 1295 Dihedral : 7.002 59.881 1339 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.40 % Allowed : 24.82 % Favored : 70.78 % 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: 0.56 (0.27), residues: 984 helix: 1.51 (0.21), residues: 587 sheet: -0.44 (0.81), residues: 48 loop : -1.52 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 373 HIS 0.002 0.000 HIS A1085 PHE 0.025 0.002 PHE A 786 TYR 0.020 0.001 TYR A 190 ARG 0.013 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 144 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5472 (t80) REVERT: A 270 LYS cc_start: 0.9218 (mtpp) cc_final: 0.8906 (mtpt) REVERT: A 314 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: A 321 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6813 (ptp) REVERT: A 349 MET cc_start: 0.7965 (mtt) cc_final: 0.7695 (mtt) REVERT: A 479 ILE cc_start: 0.9277 (mt) cc_final: 0.9040 (mt) REVERT: A 547 MET cc_start: 0.7537 (tpp) cc_final: 0.6826 (mmp) REVERT: A 588 ARG cc_start: 0.7668 (tmm-80) cc_final: 0.6465 (mpt180) REVERT: A 797 ASP cc_start: 0.8035 (p0) cc_final: 0.7508 (p0) REVERT: A 901 ASN cc_start: 0.8420 (t0) cc_final: 0.8187 (t0) REVERT: A 1131 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6086 (p90) outliers start: 31 outliers final: 23 residues processed: 136 average time/residue: 0.1737 time to fit residues: 33.4237 Evaluate side-chains 139 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 167 SER 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 321 MET 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 440 CYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1038 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 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 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 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 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7674 Z= 0.198 Angle : 0.600 9.959 10512 Z= 0.298 Chirality : 0.040 0.212 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.906 59.487 1339 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.82 % Allowed : 25.11 % Favored : 70.07 % 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: 0.60 (0.27), residues: 984 helix: 1.56 (0.21), residues: 588 sheet: -0.53 (0.81), residues: 48 loop : -1.54 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.002 0.001 HIS A 936 PHE 0.021 0.001 PHE A 408 TYR 0.025 0.001 TYR A 190 ARG 0.014 0.000 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 149 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5458 (t80) REVERT: A 270 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8907 (mtpt) REVERT: A 314 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: A 321 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6804 (ptp) REVERT: A 349 MET cc_start: 0.7947 (mtt) cc_final: 0.7686 (mtt) REVERT: A 479 ILE cc_start: 0.9283 (mt) cc_final: 0.9049 (mt) REVERT: A 547 MET cc_start: 0.7519 (tpp) cc_final: 0.6774 (mmp) REVERT: A 588 ARG cc_start: 0.7667 (tmm-80) cc_final: 0.6465 (mpt180) REVERT: A 797 ASP cc_start: 0.7935 (p0) cc_final: 0.7424 (p0) REVERT: A 901 ASN cc_start: 0.8419 (t0) cc_final: 0.8183 (t0) REVERT: A 1131 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6037 (p90) outliers start: 34 outliers final: 25 residues processed: 143 average time/residue: 0.1686 time to fit residues: 33.8745 Evaluate side-chains 141 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 167 SER 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 321 MET 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 440 CYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1038 THR 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 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 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.243110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.201825 restraints weight = 7943.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.200359 restraints weight = 9895.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.203590 restraints weight = 7311.736| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7674 Z= 0.207 Angle : 0.610 9.920 10512 Z= 0.304 Chirality : 0.041 0.199 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.876 59.407 1338 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.26 % Allowed : 25.53 % Favored : 70.21 % 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: 0.62 (0.27), residues: 984 helix: 1.58 (0.21), residues: 588 sheet: -0.49 (0.81), residues: 48 loop : -1.54 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 115 HIS 0.004 0.001 HIS A 936 PHE 0.023 0.002 PHE A 786 TYR 0.024 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: 1765.47 seconds wall clock time: 32 minutes 45.02 seconds (1965.02 seconds total)