Starting phenix.real_space_refine on Tue Feb 13 17:40:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_2024/7v6z_31754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_2024/7v6z_31754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_2024/7v6z_31754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_2024/7v6z_31754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/02_2024/7v6z_31754_updated.pdb" } 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 Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.62, per 1000 atoms: 0.65 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 - 3.50 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 A1201 " - " ASN A 127 " " NAG A1202 " - " ASN A 335 " " NAG A1203 " - " ASN A 400 " " NAG B 1 " - " ASN A 986 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 38 helices and 2 sheets defined 59.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 61 through 103 removed outlier: 5.665A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) 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) removed outlier: 3.919A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' 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 217 through 220 Processing helix chain 'A' and resid 222 through 227 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 262 through 270 Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.586A pdb=" N ALA A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 483 through 513 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 524 through 550 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) removed outlier: 3.772A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 590 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 718 through 731 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 733 through 755 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) Processing helix chain 'A' and resid 763 through 766 No H-bonds generated for 'chain 'A' and resid 763 through 766' Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 830 through 851 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 875 through 879 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 970 through 989 Processing helix chain 'A' and resid 999 through 1033 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 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1091 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 1097 through 1128 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) removed outlier: 4.417A pdb=" N GLY A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1163 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) removed outlier: 4.123A pdb=" N LEU A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A1155 " --> pdb=" O LEU A1151 " (cutoff:3.500A) 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= A, first strand: chain 'A' and resid 345 through 351 Processing sheet with id= B, first strand: chain 'A' and resid 957 through 965 418 hydrogen bonds defined for protein. 1242 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: 2.08 Time building geometry restraints manager: 3.42 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: 97.57 - 105.31: 229 105.31 - 113.04: 3865 113.04 - 120.77: 3837 120.77 - 128.50: 1965 128.50 - 136.23: 76 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: 2316 2.81 - 3.33: 7624 3.33 - 3.85: 11869 3.85 - 4.38: 13719 4.38 - 4.90: 21288 Nonbonded interactions: 56816 Sorted by model distance: nonbonded pdb=" O GLY A1115 " pdb=" OG SER A1118 " model vdw 2.282 2.440 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 56811 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: 1.270 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: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- 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= 0.794 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 fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 0.820 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: 0.1610 time to fit residues: 54.2176 Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 51 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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 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: 0.7038 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7248 Z= 0.232 Angle : 0.692 7.993 9972 Z= 0.361 Chirality : 0.045 0.231 1247 Planarity : 0.006 0.065 1251 Dihedral : 8.017 57.940 1266 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 8.24 % Allowed : 15.97 % Favored : 75.80 % 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: 1.15 (0.26), residues: 1000 helix: 1.89 (0.21), residues: 588 sheet: -0.06 (0.73), residues: 48 loop : -1.04 (0.31), residues: 364 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 0.025 0.002 PHE A 776 TYR 0.017 0.002 TYR A 190 ARG 0.004 0.001 ARG A 756 *********************** 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 202 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 CYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5982 (t) REVERT: A 573 MET cc_start: 0.8316 (tmm) cc_final: 0.8007 (tmm) REVERT: A 771 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7190 (m) REVERT: A 972 ASP cc_start: 0.7926 (m-30) cc_final: 0.7598 (t0) REVERT: A 984 CYS cc_start: 0.7662 (m) cc_final: 0.7177 (t) REVERT: A 1099 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.5602 (t70) outliers start: 49 outliers final: 29 residues processed: 185 average time/residue: 0.1463 time to fit residues: 40.1797 Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 344 HIS 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 771 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 926 ASN Chi-restraints excluded: chain A residue 955 ILE 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: 1.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A1152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7248 Z= 0.233 Angle : 0.656 10.266 9972 Z= 0.336 Chirality : 0.043 0.203 1247 Planarity : 0.005 0.053 1251 Dihedral : 6.932 53.541 1250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 9.24 % Allowed : 17.65 % Favored : 73.11 % 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: 1.11 (0.27), residues: 1000 helix: 1.85 (0.21), residues: 587 sheet: -0.43 (0.72), residues: 49 loop : -0.96 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 837 HIS 0.005 0.001 HIS A 175 PHE 0.017 0.002 PHE A1133 TYR 0.019 0.002 TYR A 179 ARG 0.004 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 201 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8421 (tp) cc_final: 0.8142 (tt) REVERT: A 504 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 526 CYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6004 (t) REVERT: A 573 MET cc_start: 0.8397 (tmm) cc_final: 0.8175 (tmm) REVERT: A 771 THR cc_start: 0.7503 (m) cc_final: 0.7263 (m) REVERT: A 829 MET cc_start: 0.7839 (ptt) cc_final: 0.7634 (ptm) REVERT: A 984 CYS cc_start: 0.7712 (m) cc_final: 0.7101 (t) REVERT: A 1072 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5713 (mp) REVERT: A 1099 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5686 (t70) outliers start: 55 outliers final: 36 residues processed: 180 average time/residue: 0.1305 time to fit residues: 34.8773 Evaluate side-chains 171 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 279 ASP 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 409 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 475 SER 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 568 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 813 SER 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 1021 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET 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: 0.8980 chunk 47 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7248 Z= 0.194 Angle : 0.620 10.587 9972 Z= 0.310 Chirality : 0.042 0.227 1247 Planarity : 0.005 0.048 1251 Dihedral : 6.497 50.779 1247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 7.90 % Allowed : 20.34 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.27), residues: 1000 helix: 1.98 (0.21), residues: 583 sheet: -0.36 (0.77), residues: 44 loop : -0.99 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.004 0.001 HIS A 275 PHE 0.021 0.001 PHE A 408 TYR 0.019 0.001 TYR A 190 ARG 0.003 0.000 ARG A1100 *********************** 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 183 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7843 (t80) cc_final: 0.7478 (t80) REVERT: A 473 LEU cc_start: 0.8379 (tp) cc_final: 0.8107 (tt) REVERT: A 526 CYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5807 (t) REVERT: A 573 MET cc_start: 0.8361 (tmm) cc_final: 0.8139 (tmm) REVERT: A 828 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7718 (mm-40) REVERT: A 984 CYS cc_start: 0.7715 (m) cc_final: 0.7104 (t) REVERT: A 1099 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.5618 (t70) outliers start: 47 outliers final: 36 residues processed: 164 average time/residue: 0.1294 time to fit residues: 31.7194 Evaluate side-chains 165 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 279 ASP 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 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 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 586 LEU Chi-restraints excluded: chain A residue 764 THR 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 813 SER 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 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.1980 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7248 Z= 0.182 Angle : 0.622 10.200 9972 Z= 0.304 Chirality : 0.041 0.319 1247 Planarity : 0.005 0.046 1251 Dihedral : 6.077 49.688 1244 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 7.23 % Allowed : 22.35 % Favored : 70.42 % 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: 1.23 (0.27), residues: 1000 helix: 2.02 (0.21), residues: 585 sheet: -0.33 (0.78), residues: 44 loop : -1.03 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 115 HIS 0.006 0.001 HIS A 809 PHE 0.019 0.001 PHE A 408 TYR 0.019 0.001 TYR A 190 ARG 0.003 0.000 ARG A1100 *********************** 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 184 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8800 (mt) cc_final: 0.8585 (mp) REVERT: A 408 PHE cc_start: 0.7807 (t80) cc_final: 0.7491 (t80) REVERT: A 473 LEU cc_start: 0.8380 (tp) cc_final: 0.8092 (tt) REVERT: A 561 LEU cc_start: 0.8742 (mt) cc_final: 0.8500 (mt) REVERT: A 828 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7644 (mm-40) REVERT: A 984 CYS cc_start: 0.7737 (m) cc_final: 0.7125 (t) REVERT: A 1144 ILE cc_start: 0.8491 (tt) cc_final: 0.8163 (pt) outliers start: 43 outliers final: 34 residues processed: 165 average time/residue: 0.1334 time to fit residues: 32.9305 Evaluate side-chains 164 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 LEU 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 808 LEU Chi-restraints excluded: chain A residue 813 SER 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 1057 MET 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: 30.0000 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7248 Z= 0.278 Angle : 0.668 8.733 9972 Z= 0.337 Chirality : 0.043 0.242 1247 Planarity : 0.005 0.046 1251 Dihedral : 5.872 52.084 1239 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 8.40 % Allowed : 22.18 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.27), residues: 1000 helix: 1.62 (0.21), residues: 586 sheet: -0.54 (0.75), residues: 44 loop : -1.05 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1037 HIS 0.012 0.001 HIS A 809 PHE 0.029 0.002 PHE A 408 TYR 0.016 0.002 TYR A 957 ARG 0.005 0.001 ARG A 363 *********************** 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 200 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 150 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7859 (t80) cc_final: 0.7627 (t80) REVERT: A 473 LEU cc_start: 0.8488 (tp) cc_final: 0.8137 (tt) REVERT: A 783 TYR cc_start: 0.6876 (m-80) cc_final: 0.6563 (m-80) REVERT: A 794 GLN cc_start: 0.7714 (mt0) cc_final: 0.7382 (mt0) REVERT: A 828 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7606 (mm-40) outliers start: 50 outliers final: 37 residues processed: 181 average time/residue: 0.1277 time to fit residues: 34.5952 Evaluate side-chains 174 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 279 ASP 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 388 THR 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 423 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 567 VAL 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 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 990 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 1057 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.0770 chunk 57 optimal weight: 10.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7248 Z= 0.246 Angle : 0.651 9.860 9972 Z= 0.325 Chirality : 0.042 0.300 1247 Planarity : 0.005 0.046 1251 Dihedral : 5.663 51.157 1237 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 7.90 % Allowed : 25.04 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1000 helix: 1.67 (0.21), residues: 586 sheet: -0.70 (0.76), residues: 44 loop : -1.05 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1037 HIS 0.014 0.001 HIS A 344 PHE 0.022 0.002 PHE A 408 TYR 0.017 0.002 TYR A 190 ARG 0.003 0.000 ARG A1100 *********************** 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 190 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7788 (t80) cc_final: 0.7563 (t80) REVERT: A 473 LEU cc_start: 0.8522 (tp) cc_final: 0.7953 (tt) REVERT: A 569 PHE cc_start: 0.8048 (m-10) cc_final: 0.7683 (m-10) REVERT: A 573 MET cc_start: 0.8416 (tmm) cc_final: 0.8046 (tmm) REVERT: A 794 GLN cc_start: 0.7660 (mt0) cc_final: 0.7333 (mt0) REVERT: A 828 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7753 (mm-40) REVERT: A 1099 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5642 (t70) REVERT: A 1144 ILE cc_start: 0.8472 (tt) cc_final: 0.8233 (pt) outliers start: 47 outliers final: 40 residues processed: 175 average time/residue: 0.1346 time to fit residues: 34.6778 Evaluate side-chains 177 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 279 ASP 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 388 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL 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 506 HIS 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 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 959 GLN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 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 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1147 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 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 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7248 Z= 0.197 Angle : 0.641 10.837 9972 Z= 0.315 Chirality : 0.041 0.293 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.493 49.336 1237 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 7.06 % Allowed : 25.71 % Favored : 67.23 % 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: 0.99 (0.27), residues: 1000 helix: 1.74 (0.21), residues: 587 sheet: -0.68 (0.76), residues: 44 loop : -0.95 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1037 HIS 0.025 0.002 HIS A 344 PHE 0.034 0.002 PHE A 502 TYR 0.022 0.002 TYR A 920 ARG 0.003 0.000 ARG A1100 *********************** 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 184 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8461 (tp) cc_final: 0.8250 (tp) REVERT: A 561 LEU cc_start: 0.8755 (mt) cc_final: 0.8509 (mt) REVERT: A 569 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7666 (m-10) REVERT: A 573 MET cc_start: 0.8370 (tmm) cc_final: 0.8053 (tmm) REVERT: A 794 GLN cc_start: 0.7633 (mt0) cc_final: 0.7312 (mt0) REVERT: A 828 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7617 (mm-40) REVERT: A 949 ILE cc_start: 0.4740 (mm) cc_final: 0.4532 (mm) REVERT: A 984 CYS cc_start: 0.7834 (m) cc_final: 0.7306 (t) REVERT: A 1099 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5575 (t70) outliers start: 42 outliers final: 34 residues processed: 169 average time/residue: 0.1385 time to fit residues: 34.6564 Evaluate side-chains 168 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 279 ASP 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 388 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL 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 546 PHE 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 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 992 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 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 50.0000 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7248 Z= 0.197 Angle : 0.649 10.870 9972 Z= 0.318 Chirality : 0.041 0.312 1247 Planarity : 0.005 0.044 1251 Dihedral : 5.396 48.285 1237 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 6.05 % Allowed : 27.56 % Favored : 66.39 % 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: 0.94 (0.27), residues: 1000 helix: 1.67 (0.21), residues: 593 sheet: -0.51 (0.78), residues: 44 loop : -0.98 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1037 HIS 0.019 0.001 HIS A 344 PHE 0.054 0.002 PHE A 408 TYR 0.024 0.002 TYR A 920 ARG 0.003 0.000 ARG A1100 *********************** 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 173 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8470 (tp) cc_final: 0.8242 (tp) REVERT: A 561 LEU cc_start: 0.8740 (mt) cc_final: 0.8493 (mt) REVERT: A 569 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: A 573 MET cc_start: 0.8370 (tmm) cc_final: 0.8033 (tmm) REVERT: A 794 GLN cc_start: 0.7633 (mt0) cc_final: 0.7264 (mt0) REVERT: A 828 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7623 (mm-40) REVERT: A 984 CYS cc_start: 0.8029 (m) cc_final: 0.7359 (t) REVERT: A 1099 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5573 (t70) outliers start: 36 outliers final: 33 residues processed: 160 average time/residue: 0.1323 time to fit residues: 31.4277 Evaluate side-chains 169 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 279 ASP 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 388 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL 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 546 PHE 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 788 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 992 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 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 84 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7248 Z= 0.176 Angle : 0.653 11.140 9972 Z= 0.316 Chirality : 0.042 0.320 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.247 46.378 1237 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 5.55 % Allowed : 28.74 % Favored : 65.71 % 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: 1.03 (0.27), residues: 1000 helix: 1.76 (0.21), residues: 593 sheet: -0.40 (0.77), residues: 42 loop : -1.00 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 837 HIS 0.004 0.001 HIS A 809 PHE 0.044 0.001 PHE A 408 TYR 0.024 0.001 TYR A 920 ARG 0.003 0.000 ARG A1100 ********************** 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 173 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 87 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6801 (t80) REVERT: A 473 LEU cc_start: 0.8396 (tp) cc_final: 0.8174 (tp) REVERT: A 475 SER cc_start: 0.8191 (m) cc_final: 0.7864 (p) REVERT: A 573 MET cc_start: 0.8367 (tmm) cc_final: 0.8016 (tmm) REVERT: A 794 GLN cc_start: 0.7550 (mt0) cc_final: 0.7193 (mt0) REVERT: A 828 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7539 (mm-40) REVERT: A 1099 HIS cc_start: 0.5969 (OUTLIER) cc_final: 0.5497 (t70) outliers start: 33 outliers final: 26 residues processed: 157 average time/residue: 0.1320 time to fit residues: 30.7973 Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS 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 388 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 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 764 THR 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 1012 HIS 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 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124407 restraints weight = 12021.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128451 restraints weight = 6187.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.131282 restraints weight = 4114.023| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7248 Z= 0.241 Angle : 0.677 10.043 9972 Z= 0.335 Chirality : 0.043 0.309 1247 Planarity : 0.005 0.044 1251 Dihedral : 5.250 48.620 1237 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 5.04 % Allowed : 30.59 % Favored : 64.37 % 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: 0.97 (0.27), residues: 1000 helix: 1.66 (0.21), residues: 594 sheet: -0.24 (0.78), residues: 42 loop : -0.95 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1037 HIS 0.005 0.001 HIS A 809 PHE 0.049 0.002 PHE A 408 TYR 0.021 0.002 TYR A 920 ARG 0.003 0.000 ARG A 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1703.54 seconds wall clock time: 31 minutes 34.82 seconds (1894.82 seconds total)