Starting phenix.real_space_refine on Sat Dec 28 01:38:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.map" model { file = "/net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6z_31754/12_2024/7v6z_31754.cif" } resolution = 3.64 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= 0.048 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4626 2.51 5 N 1195 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7082 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 6984 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 45, 'TRANS': 962} Chain breaks: 3 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1278 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 36, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 660 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.35, per 1000 atoms: 0.61 Number of scatterers: 7082 At special positions: 0 Unit cell: (88.56, 88.56, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1229 8.00 N 1195 7.00 C 4626 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=2.05 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=2.02 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 A1201 " - " ASN A 127 " " NAG A1202 " - " ASN A 335 " " NAG A1203 " - " ASN A 400 " " NAG B 1 " - " ASN A 986 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 725.7 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 66.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 60 through 83 Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.831A pdb=" N LEU A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.124A pdb=" N LYS A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 228' Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.561A pdb=" N ARG A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.838A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 397 removed outlier: 3.586A pdb=" N ALA A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.649A pdb=" N LEU A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 444 Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 482 through 514 removed outlier: 3.865A pdb=" N LEU A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.683A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 549 removed outlier: 4.354A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 591 removed outlier: 3.891A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 717 through 732 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 756 removed outlier: 3.753A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 756 " --> pdb=" O TYR A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 removed outlier: 4.142A pdb=" N ILE A 766 " --> pdb=" O ASP A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.963A pdb=" N TYR A 806 " --> pdb=" O GLN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 852 Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 904 through 915 Processing helix chain 'A' and resid 916 through 924 removed outlier: 4.257A pdb=" N TYR A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 990 Processing helix chain 'A' and resid 999 through 1034 removed outlier: 3.571A pdb=" N PHE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A1005 " --> pdb=" O PHE A1001 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLN A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1008 " --> pdb=" O TRP A1004 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1061 Processing helix chain 'A' and resid 1065 through 1092 removed outlier: 3.608A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1127 removed outlier: 3.520A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 3.555A pdb=" N GLY A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1152 removed outlier: 3.742A pdb=" N VAL A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 Proline residue: A1158 - end of helix removed outlier: 3.543A pdb=" N PHE A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) 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 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'A' and resid 957 through 965 485 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1118 1.31 - 1.44: 2015 1.44 - 1.57: 4064 1.57 - 1.70: 1 1.70 - 1.83: 50 Bond restraints: 7248 Sorted by residual: bond pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.26e-02 6.30e+03 4.50e+01 bond pdb=" C VAL A 393 " pdb=" O VAL A 393 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.17e-02 7.31e+03 4.24e+01 bond pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 4.01e+01 bond pdb=" N SER A 172 " pdb=" CA SER A 172 " ideal model delta sigma weight residual 1.459 1.386 0.073 1.21e-02 6.83e+03 3.64e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.30e-02 5.92e+03 3.27e+01 ... (remaining 7243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 8964 2.46 - 4.92: 773 4.92 - 7.38: 173 7.38 - 9.84: 50 9.84 - 12.30: 12 Bond angle restraints: 9972 Sorted by residual: angle pdb=" N LYS A 297 " pdb=" CA LYS A 297 " pdb=" C LYS A 297 " ideal model delta sigma weight residual 111.28 99.40 11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LEU A 594 " pdb=" CA LEU A 594 " pdb=" C LEU A 594 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N TYR A 210 " pdb=" CA TYR A 210 " pdb=" C TYR A 210 " ideal model delta sigma weight residual 109.72 98.10 11.62 1.25e+00 6.40e-01 8.65e+01 angle pdb=" N SER A 40 " pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 111.74 99.44 12.30 1.35e+00 5.49e-01 8.30e+01 angle pdb=" N PHE A 729 " pdb=" CA PHE A 729 " pdb=" C PHE A 729 " ideal model delta sigma weight residual 111.07 102.04 9.03 1.07e+00 8.73e-01 7.12e+01 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3939 17.94 - 35.89: 263 35.89 - 53.83: 91 53.83 - 71.77: 17 71.77 - 89.71: 3 Dihedral angle restraints: 4313 sinusoidal: 1386 harmonic: 2927 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 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -36.82 -49.18 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" C ILE A 777 " pdb=" N ILE A 777 " pdb=" CA ILE A 777 " pdb=" CB ILE A 777 " ideal model delta harmonic sigma weight residual -122.00 -136.26 14.26 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 4310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 975 0.120 - 0.239: 206 0.239 - 0.359: 49 0.359 - 0.479: 13 0.479 - 0.598: 4 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA TRP A1004 " pdb=" N TRP A1004 " pdb=" C TRP A1004 " pdb=" CB TRP A1004 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA ILE A 777 " pdb=" N ILE A 777 " pdb=" C ILE A 777 " pdb=" CB ILE A 777 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA LEU A 594 " pdb=" N LEU A 594 " pdb=" C LEU A 594 " pdb=" CB LEU A 594 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 1244 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.098 5.00e-02 4.00e+02 1.47e-01 3.47e+01 pdb=" N PRO A1158 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1153 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C GLY A1153 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A1153 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A1154 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 294 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 295 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.060 5.00e-02 4.00e+02 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2308 2.81 - 3.33: 7578 3.33 - 3.85: 11798 3.85 - 4.38: 13600 4.38 - 4.90: 21272 Nonbonded interactions: 56556 Sorted by model distance: nonbonded pdb=" O GLY A1115 " pdb=" OG SER A1118 " model vdw 2.282 3.040 nonbonded pdb=" CG2 ILE A1071 " pdb=" CD1 ILE A1071 " model vdw 2.314 3.104 nonbonded pdb=" N SER A1065 " pdb=" O SER A1065 " model vdw 2.354 2.496 nonbonded pdb=" N ASP A 591 " pdb=" O ASP A 591 " model vdw 2.410 2.496 nonbonded pdb=" N ARG A 772 " pdb=" N GLU A 773 " model vdw 2.436 2.560 ... (remaining 56551 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 : 0.012 0.085 7248 Z= 0.798 Angle : 1.666 12.301 9972 Z= 1.164 Chirality : 0.114 0.598 1247 Planarity : 0.010 0.147 1251 Dihedral : 14.342 88.724 2412 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.20 % Favored : 96.50 % Rotamer: Outliers : 10.76 % Allowed : 8.91 % Favored : 80.34 % Cbeta Deviations : 0.63 % 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: 1.70 (0.27), residues: 1000 helix: 2.51 (0.22), residues: 581 sheet: 0.56 (0.75), residues: 47 loop : -1.15 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 837 HIS 0.007 0.002 HIS A 164 PHE 0.023 0.002 PHE A1131 TYR 0.035 0.003 TYR A 774 ARG 0.005 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7940 (t80) cc_final: 0.7585 (t80) REVERT: A 771 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7237 (m) REVERT: A 829 MET cc_start: 0.7569 (ptp) cc_final: 0.7358 (ptp) REVERT: A 984 CYS cc_start: 0.7857 (m) cc_final: 0.7546 (t) REVERT: A 1099 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5894 (t70) outliers start: 64 outliers final: 22 residues processed: 243 average time/residue: 0.1619 time to fit residues: 54.5102 Evaluate side-chains 162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1150 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 154 ASN A 175 HIS ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 296 ASN A 386 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A1006 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7248 Z= 0.244 Angle : 0.719 7.884 9972 Z= 0.381 Chirality : 0.046 0.234 1247 Planarity : 0.006 0.064 1251 Dihedral : 7.944 56.892 1266 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 8.07 % Allowed : 16.81 % Favored : 75.13 % 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: 1.03 (0.26), residues: 1000 helix: 1.80 (0.21), residues: 594 sheet: -0.23 (0.70), residues: 49 loop : -1.12 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 837 HIS 0.008 0.001 HIS A 809 PHE 0.019 0.002 PHE A 786 TYR 0.024 0.002 TYR A 179 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 526 CYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6013 (t) REVERT: A 573 MET cc_start: 0.8279 (tmm) cc_final: 0.7952 (tmm) REVERT: A 832 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7480 (m170) REVERT: A 972 ASP cc_start: 0.7961 (m-30) cc_final: 0.7632 (t0) REVERT: A 984 CYS cc_start: 0.7760 (m) cc_final: 0.7286 (t) REVERT: A 1099 HIS cc_start: 0.5924 (OUTLIER) cc_final: 0.5400 (t70) outliers start: 48 outliers final: 29 residues processed: 184 average time/residue: 0.1365 time to fit residues: 37.6214 Evaluate side-chains 162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7248 Z= 0.205 Angle : 0.678 10.246 9972 Z= 0.346 Chirality : 0.044 0.200 1247 Planarity : 0.005 0.053 1251 Dihedral : 6.732 52.501 1249 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 9.58 % Allowed : 18.49 % Favored : 71.93 % 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: 1.01 (0.27), residues: 1000 helix: 1.80 (0.21), residues: 594 sheet: -0.35 (0.74), residues: 44 loop : -1.14 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 837 HIS 0.007 0.001 HIS A 832 PHE 0.016 0.002 PHE A 905 TYR 0.020 0.002 TYR A 179 ARG 0.005 0.001 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASP cc_start: 0.6582 (m-30) cc_final: 0.6314 (m-30) REVERT: A 473 LEU cc_start: 0.8412 (tp) cc_final: 0.8110 (tt) REVERT: A 504 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8532 (tt) REVERT: A 526 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6230 (t) REVERT: A 573 MET cc_start: 0.8359 (tmm) cc_final: 0.8134 (tmm) REVERT: A 959 GLN cc_start: 0.8136 (pt0) cc_final: 0.7930 (pt0) REVERT: A 984 CYS cc_start: 0.7788 (m) cc_final: 0.7286 (t) REVERT: A 1072 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5703 (mp) REVERT: A 1099 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5280 (t70) outliers start: 57 outliers final: 31 residues processed: 174 average time/residue: 0.1325 time to fit residues: 34.6526 Evaluate side-chains 161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7248 Z= 0.281 Angle : 0.687 9.555 9972 Z= 0.352 Chirality : 0.044 0.204 1247 Planarity : 0.005 0.050 1251 Dihedral : 6.502 53.998 1246 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 10.25 % Allowed : 18.15 % Favored : 71.60 % 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: 0.66 (0.27), residues: 1000 helix: 1.43 (0.21), residues: 601 sheet: -0.54 (0.75), residues: 44 loop : -1.14 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.010 0.001 HIS A 809 PHE 0.037 0.002 PHE A 408 TYR 0.017 0.002 TYR A 179 ARG 0.004 0.001 ARG A 981 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 CYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6264 (t) REVERT: A 774 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 984 CYS cc_start: 0.7961 (m) cc_final: 0.7280 (t) REVERT: A 1099 HIS cc_start: 0.5941 (OUTLIER) cc_final: 0.5478 (t70) REVERT: A 1152 ASN cc_start: 0.7759 (t0) cc_final: 0.7495 (t0) outliers start: 61 outliers final: 40 residues processed: 181 average time/residue: 0.1398 time to fit residues: 38.6399 Evaluate side-chains 173 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1013 TRP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1147 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 344 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7248 Z= 0.226 Angle : 0.666 9.154 9972 Z= 0.335 Chirality : 0.043 0.219 1247 Planarity : 0.005 0.048 1251 Dihedral : 6.270 52.385 1245 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 7.23 % Allowed : 23.87 % Favored : 68.91 % 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: 0.75 (0.26), residues: 1000 helix: 1.58 (0.21), residues: 595 sheet: -0.80 (0.70), residues: 44 loop : -1.17 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1037 HIS 0.015 0.001 HIS A 344 PHE 0.039 0.002 PHE A 408 TYR 0.019 0.002 TYR A 920 ARG 0.002 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 475 SER cc_start: 0.8282 (m) cc_final: 0.7868 (p) REVERT: A 526 CYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5814 (t) REVERT: A 774 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6814 (t80) REVERT: A 783 TYR cc_start: 0.7684 (m-80) cc_final: 0.7426 (m-10) REVERT: A 984 CYS cc_start: 0.7900 (m) cc_final: 0.7512 (t) REVERT: A 1099 HIS cc_start: 0.5850 (OUTLIER) cc_final: 0.5412 (t70) outliers start: 43 outliers final: 35 residues processed: 170 average time/residue: 0.1332 time to fit residues: 34.1926 Evaluate side-chains 172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 93 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7248 Z= 0.187 Angle : 0.635 9.646 9972 Z= 0.316 Chirality : 0.042 0.242 1247 Planarity : 0.005 0.047 1251 Dihedral : 5.908 51.330 1242 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 7.73 % Allowed : 23.87 % Favored : 68.40 % 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: 0.90 (0.27), residues: 1000 helix: 1.69 (0.21), residues: 594 sheet: -0.47 (0.71), residues: 42 loop : -1.14 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1037 HIS 0.012 0.001 HIS A 344 PHE 0.034 0.001 PHE A 408 TYR 0.019 0.002 TYR A 190 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8440 (tp) cc_final: 0.8107 (tp) REVERT: A 475 SER cc_start: 0.8202 (m) cc_final: 0.7822 (p) REVERT: A 569 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: A 573 MET cc_start: 0.8395 (tmm) cc_final: 0.8094 (tmm) REVERT: A 774 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 984 CYS cc_start: 0.7976 (m) cc_final: 0.7565 (t) REVERT: A 1099 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.5402 (t70) REVERT: A 1144 ILE cc_start: 0.8494 (tt) cc_final: 0.8228 (pt) outliers start: 46 outliers final: 36 residues processed: 167 average time/residue: 0.1362 time to fit residues: 33.9144 Evaluate side-chains 169 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1099 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7248 Z= 0.320 Angle : 0.696 8.101 9972 Z= 0.360 Chirality : 0.044 0.245 1247 Planarity : 0.005 0.046 1251 Dihedral : 6.020 53.786 1241 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 8.24 % Allowed : 23.70 % Favored : 68.07 % 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: 0.47 (0.26), residues: 1000 helix: 1.32 (0.21), residues: 601 sheet: -0.77 (0.72), residues: 42 loop : -1.29 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1037 HIS 0.006 0.001 HIS A 344 PHE 0.042 0.002 PHE A 408 TYR 0.020 0.002 TYR A 783 ARG 0.002 0.001 ARG A 981 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8588 (tt) REVERT: A 569 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: A 573 MET cc_start: 0.8319 (tmm) cc_final: 0.8029 (tmm) REVERT: A 1144 ILE cc_start: 0.8556 (tt) cc_final: 0.8261 (pt) outliers start: 49 outliers final: 37 residues processed: 168 average time/residue: 0.1418 time to fit residues: 35.4328 Evaluate side-chains 165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7248 Z= 0.206 Angle : 0.671 9.705 9972 Z= 0.334 Chirality : 0.042 0.288 1247 Planarity : 0.005 0.046 1251 Dihedral : 5.606 51.145 1237 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 6.39 % Allowed : 27.06 % Favored : 66.55 % 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: 0.80 (0.27), residues: 1000 helix: 1.62 (0.21), residues: 600 sheet: -0.69 (0.72), residues: 42 loop : -1.20 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.005 0.001 HIS A 809 PHE 0.037 0.002 PHE A 408 TYR 0.019 0.002 TYR A 787 ARG 0.002 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 569 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: A 573 MET cc_start: 0.8319 (tmm) cc_final: 0.8033 (tmm) REVERT: A 774 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 949 ILE cc_start: 0.4831 (mm) cc_final: 0.4626 (mm) REVERT: A 1144 ILE cc_start: 0.8434 (tt) cc_final: 0.8196 (pt) outliers start: 38 outliers final: 29 residues processed: 159 average time/residue: 0.1383 time to fit residues: 32.4975 Evaluate side-chains 166 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 455 VAL 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 586 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 0.0010 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7248 Z= 0.192 Angle : 0.661 9.810 9972 Z= 0.327 Chirality : 0.042 0.290 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.472 50.107 1237 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 5.55 % Allowed : 29.41 % Favored : 65.04 % 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: 0.82 (0.27), residues: 1000 helix: 1.60 (0.21), residues: 607 sheet: -0.52 (0.73), residues: 42 loop : -1.20 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1037 HIS 0.004 0.001 HIS A 809 PHE 0.036 0.001 PHE A 408 TYR 0.020 0.002 TYR A 920 ARG 0.002 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6227 (t80) REVERT: A 475 SER cc_start: 0.8194 (m) cc_final: 0.7797 (p) REVERT: A 573 MET cc_start: 0.8301 (tmm) cc_final: 0.8031 (tmm) REVERT: A 774 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6581 (t80) outliers start: 33 outliers final: 26 residues processed: 156 average time/residue: 0.1323 time to fit residues: 31.1856 Evaluate side-chains 164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7248 Z= 0.187 Angle : 0.674 10.219 9972 Z= 0.330 Chirality : 0.042 0.295 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.368 49.291 1237 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 4.54 % Allowed : 30.76 % Favored : 64.71 % 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: 0.88 (0.27), residues: 1000 helix: 1.62 (0.21), residues: 611 sheet: -0.34 (0.76), residues: 42 loop : -1.20 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 PHE 0.035 0.001 PHE A 408 TYR 0.018 0.002 TYR A 190 ARG 0.002 0.000 ARG A 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 473 LEU cc_start: 0.7935 (tp) cc_final: 0.7729 (tt) REVERT: A 475 SER cc_start: 0.8160 (m) cc_final: 0.7823 (p) REVERT: A 561 LEU cc_start: 0.8699 (mt) cc_final: 0.8484 (mt) REVERT: A 573 MET cc_start: 0.8280 (tmm) cc_final: 0.8004 (tmm) REVERT: A 774 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6586 (t80) outliers start: 27 outliers final: 24 residues processed: 154 average time/residue: 0.1330 time to fit residues: 31.1489 Evaluate side-chains 164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.156565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121525 restraints weight = 12150.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125549 restraints weight = 6293.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.128257 restraints weight = 4186.065| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7248 Z= 0.310 Angle : 0.725 10.080 9972 Z= 0.362 Chirality : 0.044 0.272 1247 Planarity : 0.005 0.044 1251 Dihedral : 5.532 53.299 1237 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 5.55 % Allowed : 30.59 % Favored : 63.87 % 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: 1000 helix: 1.44 (0.21), residues: 607 sheet: -0.51 (0.76), residues: 42 loop : -1.31 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1037 HIS 0.004 0.001 HIS A 809 PHE 0.043 0.002 PHE A 408 TYR 0.017 0.002 TYR A 190 ARG 0.002 0.000 ARG A 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.50 seconds wall clock time: 32 minutes 20.78 seconds (1940.78 seconds total)