Starting phenix.real_space_refine on Wed Feb 12 05:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6z_31754/02_2025/7v6z_31754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6z_31754/02_2025/7v6z_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_31754/02_2025/7v6z_31754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6z_31754/02_2025/7v6z_31754.map" model { file = "/net/cci-nas-00/data/ceres_data/7v6z_31754/02_2025/7v6z_31754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6z_31754/02_2025/7v6z_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.77, per 1000 atoms: 0.67 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: 2.14 Conformation dependent library (CDL) restraints added in 922.0 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: 0.79 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: 2.32 Time building geometry restraints manager: 2.41 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: 1.180 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- 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 : 0.712 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: 0.1606 time to fit residues: 54.1433 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 : 0.755 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128237 restraints weight = 11773.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132855 restraints weight = 5819.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135921 restraints weight = 3753.720| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.745 Fit side-chains revert: symmetry clash REVERT: A 526 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5971 (t) REVERT: A 573 MET cc_start: 0.8210 (tmm) cc_final: 0.7875 (tmm) REVERT: A 832 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7535 (m170) REVERT: A 959 GLN cc_start: 0.8359 (pt0) cc_final: 0.8154 (pt0) REVERT: A 972 ASP cc_start: 0.8157 (m-30) cc_final: 0.7735 (t0) REVERT: A 984 CYS cc_start: 0.7831 (m) cc_final: 0.7293 (t) REVERT: A 1099 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5464 (t70) outliers start: 48 outliers final: 29 residues processed: 184 average time/residue: 0.1325 time to fit residues: 36.1044 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 : 0.754 ------------------------------------------------------------------------------- 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 36 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.161494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126392 restraints weight = 12009.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130916 restraints weight = 5894.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133886 restraints weight = 3789.525| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3131 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= 0.239 Angle : 0.687 10.127 9972 Z= 0.353 Chirality : 0.044 0.206 1247 Planarity : 0.005 0.053 1251 Dihedral : 6.841 52.291 1249 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 10.42 % Allowed : 17.48 % Favored : 72.10 % 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: 0.93 (0.27), residues: 1000 helix: 1.73 (0.21), residues: 594 sheet: -0.52 (0.69), residues: 49 loop : -1.13 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 837 HIS 0.004 0.001 HIS A 809 PHE 0.016 0.002 PHE A1133 TYR 0.022 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 198 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8488 (tp) cc_final: 0.8220 (tt) REVERT: A 504 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8526 (tt) REVERT: A 526 CYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6113 (t) REVERT: A 573 MET cc_start: 0.8278 (tmm) cc_final: 0.8028 (tmm) REVERT: A 984 CYS cc_start: 0.7896 (m) cc_final: 0.7288 (t) REVERT: A 1072 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5421 (mp) REVERT: A 1099 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5421 (t70) outliers start: 62 outliers final: 38 residues processed: 173 average time/residue: 0.1323 time to fit residues: 34.2001 Evaluate side-chains 169 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 455 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 568 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR 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 955 ILE Chi-restraints excluded: chain A residue 965 ASN 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 1013 TRP 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 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 20 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 59 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 314 GLN ** A 570 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 = 0.4275 r_free = 0.4275 target = 0.163621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128764 restraints weight = 12118.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.133464 restraints weight = 5857.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136503 restraints weight = 3737.169| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3605 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= 0.197 Angle : 0.652 12.431 9972 Z= 0.326 Chirality : 0.043 0.207 1247 Planarity : 0.005 0.048 1251 Dihedral : 6.334 51.669 1246 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Rotamer: Outliers : 7.06 % Allowed : 21.18 % 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: 1.04 (0.27), residues: 1000 helix: 1.81 (0.21), residues: 595 sheet: -0.48 (0.77), residues: 44 loop : -1.08 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.008 0.001 HIS A 809 PHE 0.020 0.001 PHE A 408 TYR 0.017 0.002 TYR A 190 ARG 0.003 0.000 ARG A 756 *********************** 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 187 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.862 Fit side-chains REVERT: A 403 GLN cc_start: 0.6844 (mp10) cc_final: 0.6618 (mp10) REVERT: A 408 PHE cc_start: 0.7795 (t80) cc_final: 0.7473 (t80) REVERT: A 422 ASP cc_start: 0.7766 (m-30) cc_final: 0.7428 (m-30) REVERT: A 475 SER cc_start: 0.8258 (m) cc_final: 0.7938 (p) REVERT: A 526 CYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6091 (t) REVERT: A 573 MET cc_start: 0.8234 (tmm) cc_final: 0.8015 (tmm) REVERT: A 972 ASP cc_start: 0.8155 (m-30) cc_final: 0.7844 (t0) REVERT: A 984 CYS cc_start: 0.7936 (m) cc_final: 0.7395 (t) REVERT: A 1099 HIS cc_start: 0.5892 (OUTLIER) cc_final: 0.5446 (t70) outliers start: 42 outliers final: 29 residues processed: 171 average time/residue: 0.1339 time to fit residues: 34.3688 Evaluate side-chains 163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 494 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 789 MET Chi-restraints excluded: chain A residue 792 VAL 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 31 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 344 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.159830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.124595 restraints weight = 11980.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.128895 restraints weight = 6022.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131739 restraints weight = 3927.821| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7248 Z= 0.261 Angle : 0.677 8.792 9972 Z= 0.342 Chirality : 0.043 0.207 1247 Planarity : 0.005 0.047 1251 Dihedral : 6.121 52.722 1243 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 8.24 % Allowed : 22.35 % 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: 0.81 (0.27), residues: 1000 helix: 1.61 (0.21), residues: 595 sheet: -0.82 (0.73), residues: 44 loop : -1.13 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1037 HIS 0.014 0.001 HIS A 344 PHE 0.024 0.002 PHE A 408 TYR 0.019 0.002 TYR A 920 ARG 0.003 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 190 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7790 (t80) cc_final: 0.7554 (t80) REVERT: A 475 SER cc_start: 0.8279 (m) cc_final: 0.7937 (p) REVERT: A 774 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 972 ASP cc_start: 0.8175 (m-30) cc_final: 0.7860 (t0) REVERT: A 984 CYS cc_start: 0.7986 (m) cc_final: 0.7314 (t) REVERT: A 1099 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.5573 (t70) REVERT: A 1144 ILE cc_start: 0.8414 (tt) cc_final: 0.8067 (pt) REVERT: A 1152 ASN cc_start: 0.7861 (t0) cc_final: 0.7607 (t0) outliers start: 49 outliers final: 40 residues processed: 170 average time/residue: 0.1275 time to fit residues: 32.5459 Evaluate side-chains 176 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 397 VAL 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 461 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 VAL 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 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 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1015 LEU 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 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 Chi-restraints excluded: chain A residue 1147 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.5967 > 50: distance: 28 - 31: 21.258 distance: 31 - 32: 7.875 distance: 32 - 33: 19.938 distance: 32 - 35: 14.020 distance: 33 - 34: 10.745 distance: 33 - 36: 41.868 distance: 36 - 37: 22.029 distance: 37 - 38: 24.151 distance: 37 - 40: 26.335 distance: 38 - 39: 32.691 distance: 38 - 41: 37.515 distance: 41 - 42: 32.240 distance: 42 - 43: 43.392 distance: 42 - 45: 20.309 distance: 43 - 44: 15.669 distance: 43 - 46: 3.786 distance: 46 - 47: 8.292 distance: 47 - 48: 21.537 distance: 47 - 50: 3.334 distance: 48 - 49: 20.272 distance: 48 - 51: 14.465 distance: 51 - 52: 15.583 distance: 52 - 53: 33.671 distance: 52 - 55: 15.827 distance: 53 - 54: 9.395 distance: 53 - 56: 31.717 distance: 56 - 57: 30.602 distance: 57 - 58: 32.888 distance: 57 - 60: 26.933 distance: 58 - 59: 26.538 distance: 58 - 61: 15.282 distance: 61 - 62: 19.263 distance: 62 - 63: 16.045 distance: 62 - 65: 20.357 distance: 63 - 64: 11.304 distance: 63 - 66: 40.158 distance: 66 - 67: 24.204 distance: 67 - 68: 10.090 distance: 68 - 69: 13.370 distance: 68 - 70: 26.215 distance: 70 - 71: 18.820 distance: 71 - 72: 42.105 distance: 71 - 74: 9.124 distance: 72 - 73: 17.573 distance: 72 - 78: 9.786 distance: 74 - 75: 20.191 distance: 74 - 76: 35.466 distance: 75 - 77: 13.956 distance: 78 - 79: 22.838 distance: 79 - 80: 14.040 distance: 79 - 82: 15.947 distance: 80 - 81: 14.306 distance: 80 - 86: 23.586 distance: 82 - 83: 19.482 distance: 82 - 84: 26.518 distance: 83 - 85: 22.508