Starting phenix.real_space_refine on Tue Apr 29 21:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.map" model { file = "/net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y81_39029/04_2025/8y81_39029.cif" } resolution = 2.89 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= -0.001 sd= 0.058 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 40 5.16 5 C 5713 2.51 5 N 1483 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1729 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2602 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2571 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: 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: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.52, per 1000 atoms: 0.62 Number of scatterers: 8915 At special positions: 0 Unit cell: (148.73, 101.65, 112.35, 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 40 16.00 O 1679 8.00 N 1483 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.05 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 112 " - pdb=" SG CYS F 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 334 " - pdb=" SG CYS E 396 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 184 " distance=2.03 Simple disulfide: pdb=" SG CYS F 230 " - pdb=" SG CYS F 289 " distance=2.02 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 396 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 301 " - " ASN A 158 " " NAG A 302 " - " ASN A 167 " " NAG D 1 " - " ASN E 265 " " NAG E 502 " - " ASN E 240 " " NAG F 501 " - " ASN F 170 " " NAG H 1 " - " ASN F 265 " " NAG T 1 " - " ASN A 65 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 19 sheets defined 29.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 213 through 231 removed outlier: 4.272A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.027A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.642A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 4.362A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.593A pdb=" N PHE B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.662A pdb=" N LEU B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 160 Processing helix chain 'B' and resid 168 through 205 removed outlier: 3.778A pdb=" N LEU B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.580A pdb=" N TRP E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'G' and resid 25 through 56 removed outlier: 3.693A pdb=" N LEU G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 48 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.538A pdb=" N ILE A 39 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TRP A 62 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.987A pdb=" N SER A 171 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS A 145 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A 173 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR A 143 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 175 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 141 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 141 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 152 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 143 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'E' and resid 104 through 109 removed outlier: 5.273A pdb=" N ALA E 163 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU E 158 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 164 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'E' and resid 209 through 213 removed outlier: 5.463A pdb=" N THR E 229 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 274 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU E 231 " --> pdb=" O SER E 272 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 272 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 233 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE E 270 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AB1, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.815A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.815A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'F' and resid 104 through 109 removed outlier: 4.765A pdb=" N ALA F 163 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR F 166 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU F 155 " --> pdb=" O TYR F 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 135 through 141 Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 213 removed outlier: 3.732A pdb=" N ASP F 234 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR F 268 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AB8, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.672A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.672A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 345 through 348 460 hydrogen bonds defined for protein. 1227 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: 2.53 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2042 1.33 - 1.45: 2026 1.45 - 1.57: 5003 1.57 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 9121 Sorted by residual: bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.63e+00 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.67e+00 bond pdb=" C1 NAG E 502 " pdb=" O5 NAG E 502 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 11953 2.42 - 4.85: 367 4.85 - 7.27: 50 7.27 - 9.70: 10 9.70 - 12.12: 3 Bond angle restraints: 12383 Sorted by residual: angle pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" CD PRO E 103 " ideal model delta sigma weight residual 112.00 104.98 7.02 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLN E 390 " pdb=" N THR E 391 " pdb=" CA THR E 391 " ideal model delta sigma weight residual 122.46 128.97 -6.51 1.41e+00 5.03e-01 2.13e+01 angle pdb=" C VAL B 127 " pdb=" N ARG B 128 " pdb=" CA ARG B 128 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C TYR E 368 " pdb=" N ASN E 369 " pdb=" CA ASN E 369 " ideal model delta sigma weight residual 125.02 132.02 -7.00 1.76e+00 3.23e-01 1.58e+01 ... (remaining 12378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5267 21.62 - 43.24: 360 43.24 - 64.85: 51 64.85 - 86.47: 28 86.47 - 108.09: 10 Dihedral angle restraints: 5716 sinusoidal: 2532 harmonic: 3184 Sorted by residual: dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual 180.00 99.19 80.81 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta harmonic sigma weight residual 180.00 140.60 39.40 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" CA ASN A 179 " pdb=" C ASN A 179 " pdb=" N LYS A 180 " pdb=" CA LYS A 180 " ideal model delta harmonic sigma weight residual 180.00 143.34 36.66 0 5.00e+00 4.00e-02 5.38e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1161 0.074 - 0.148: 254 0.148 - 0.223: 26 0.223 - 0.297: 9 0.297 - 0.371: 2 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CB ILE F 413 " pdb=" CA ILE F 413 " pdb=" CG1 ILE F 413 " pdb=" CG2 ILE F 413 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.52 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.62 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1449 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " -0.027 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C ILE A 198 " 0.092 2.00e-02 2.50e+03 pdb=" O ILE A 198 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 199 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 154 " 0.022 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR A 154 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A 154 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 154 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 154 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 154 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 154 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 154 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 33 " 0.047 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 34 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.040 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2080 2.80 - 3.32: 7809 3.32 - 3.85: 15182 3.85 - 4.37: 17784 4.37 - 4.90: 30761 Nonbonded interactions: 73616 Sorted by model distance: nonbonded pdb=" O VAL B 78 " pdb=" OG1 THR B 82 " model vdw 2.274 3.040 nonbonded pdb=" O THR B 174 " pdb=" OG1 THR B 178 " model vdw 2.274 3.040 nonbonded pdb=" O ASP E 142 " pdb=" O6 NAG D 1 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP E 143 " pdb=" ND1 HIS E 263 " model vdw 2.286 3.120 nonbonded pdb=" OH TYR C 35 " pdb=" OG1 THR G 40 " model vdw 2.287 3.040 ... (remaining 73611 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 24 through 57) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 101 through 416 or resid 502)) selection = chain 'F' } 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 individual isotropic 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: 1.640 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 22.310 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.007 0.119 9144 Z= 0.296 Angle : 1.014 12.122 12441 Z= 0.528 Chirality : 0.063 0.371 1452 Planarity : 0.007 0.073 1519 Dihedral : 16.035 108.091 3613 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.29 % 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: -1.30 (0.24), residues: 1065 helix: -1.51 (0.25), residues: 279 sheet: -0.11 (0.29), residues: 321 loop : -0.83 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.011 0.002 HIS F 295 PHE 0.036 0.003 PHE E 117 TYR 0.059 0.003 TYR A 154 ARG 0.004 0.000 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 7) link_NAG-ASN : angle 4.16850 ( 21) link_BETA1-4 : bond 0.00431 ( 5) link_BETA1-4 : angle 1.98245 ( 15) hydrogen bonds : bond 0.12190 ( 426) hydrogen bonds : angle 7.26437 ( 1227) SS BOND : bond 0.00649 ( 11) SS BOND : angle 1.56101 ( 22) covalent geometry : bond 0.00687 ( 9121) covalent geometry : angle 0.99699 (12383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 1.0651 time to fit residues: 145.0877 Evaluate side-chains 83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 134 ASN B 151 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 174 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.171626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133654 restraints weight = 10334.255| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.15 r_work: 0.3272 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9144 Z= 0.165 Angle : 0.648 10.306 12441 Z= 0.333 Chirality : 0.046 0.153 1452 Planarity : 0.005 0.062 1519 Dihedral : 11.182 75.612 1504 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.61 % Allowed : 8.27 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: -0.57 (0.24), residues: 1065 helix: -0.35 (0.27), residues: 282 sheet: -0.00 (0.29), residues: 324 loop : -0.52 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 222 HIS 0.006 0.001 HIS F 295 PHE 0.019 0.002 PHE E 117 TYR 0.017 0.001 TYR G 35 ARG 0.005 0.001 ARG E 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 7) link_NAG-ASN : angle 3.05412 ( 21) link_BETA1-4 : bond 0.00290 ( 5) link_BETA1-4 : angle 2.13932 ( 15) hydrogen bonds : bond 0.03815 ( 426) hydrogen bonds : angle 5.61736 ( 1227) SS BOND : bond 0.00476 ( 11) SS BOND : angle 0.89570 ( 22) covalent geometry : bond 0.00381 ( 9121) covalent geometry : angle 0.63159 (12383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8640 (ttp-170) cc_final: 0.8310 (ttp-170) REVERT: E 141 MET cc_start: 0.8360 (ttt) cc_final: 0.8032 (ttp) REVERT: E 372 ASN cc_start: 0.6349 (t0) cc_final: 0.6126 (t0) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 0.9692 time to fit residues: 104.4446 Evaluate side-chains 90 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 96 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN F 118 HIS F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.171742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132063 restraints weight = 10407.190| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.24 r_work: 0.3278 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9144 Z= 0.140 Angle : 0.592 10.589 12441 Z= 0.305 Chirality : 0.045 0.175 1452 Planarity : 0.004 0.059 1519 Dihedral : 9.459 73.880 1504 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.72 % Allowed : 10.80 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: -0.11 (0.25), residues: 1065 helix: 0.47 (0.29), residues: 273 sheet: 0.04 (0.29), residues: 324 loop : -0.33 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS F 295 PHE 0.016 0.002 PHE E 117 TYR 0.016 0.001 TYR G 35 ARG 0.005 0.000 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 7) link_NAG-ASN : angle 2.60736 ( 21) link_BETA1-4 : bond 0.00311 ( 5) link_BETA1-4 : angle 2.11899 ( 15) hydrogen bonds : bond 0.03550 ( 426) hydrogen bonds : angle 5.20980 ( 1227) SS BOND : bond 0.00326 ( 11) SS BOND : angle 0.72630 ( 22) covalent geometry : bond 0.00315 ( 9121) covalent geometry : angle 0.57859 (12383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8295 (ttp-170) REVERT: A 201 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8219 (mmt180) REVERT: B 100 TYR cc_start: 0.8585 (t80) cc_final: 0.8383 (t80) REVERT: E 141 MET cc_start: 0.8401 (ttt) cc_final: 0.8065 (ttp) REVERT: E 372 ASN cc_start: 0.6238 (t0) cc_final: 0.5991 (t0) REVERT: F 279 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7067 (mmtt) REVERT: G 32 LEU cc_start: 0.7499 (mt) cc_final: 0.7114 (mt) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 0.8586 time to fit residues: 101.8267 Evaluate side-chains 100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 122 GLN E 138 HIS E 153 ASN E 223 ASN E 350 GLN F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.173559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134869 restraints weight = 10199.439| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.23 r_work: 0.3257 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9144 Z= 0.157 Angle : 0.596 10.530 12441 Z= 0.304 Chirality : 0.045 0.148 1452 Planarity : 0.004 0.057 1519 Dihedral : 8.828 73.398 1504 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.12 % Allowed : 13.52 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.09 (0.25), residues: 1065 helix: 0.78 (0.30), residues: 273 sheet: 0.08 (0.29), residues: 324 loop : -0.25 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.005 0.001 HIS F 295 PHE 0.016 0.002 PHE A 207 TYR 0.016 0.001 TYR G 35 ARG 0.006 0.000 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.51524 ( 21) link_BETA1-4 : bond 0.00278 ( 5) link_BETA1-4 : angle 2.16557 ( 15) hydrogen bonds : bond 0.03473 ( 426) hydrogen bonds : angle 5.07484 ( 1227) SS BOND : bond 0.00344 ( 11) SS BOND : angle 0.77515 ( 22) covalent geometry : bond 0.00364 ( 9121) covalent geometry : angle 0.58255 (12383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8236 (ttp-170) REVERT: A 201 ARG cc_start: 0.8432 (mtt180) cc_final: 0.8215 (mmt180) REVERT: E 122 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7757 (mt0) REVERT: E 141 MET cc_start: 0.8416 (ttt) cc_final: 0.8053 (ttp) REVERT: E 338 ASN cc_start: 0.8157 (t0) cc_final: 0.7950 (t0) REVERT: E 372 ASN cc_start: 0.6261 (t0) cc_final: 0.6054 (t0) REVERT: F 185 LYS cc_start: 0.7070 (tttp) cc_final: 0.6758 (tttt) REVERT: G 32 LEU cc_start: 0.7446 (mt) cc_final: 0.7018 (mt) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 0.9195 time to fit residues: 108.4995 Evaluate side-chains 100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.173173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134316 restraints weight = 10257.732| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.25 r_work: 0.3267 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.147 Angle : 0.583 10.445 12441 Z= 0.297 Chirality : 0.044 0.145 1452 Planarity : 0.004 0.055 1519 Dihedral : 8.473 72.825 1504 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.22 % Allowed : 15.14 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.22 (0.25), residues: 1065 helix: 0.98 (0.30), residues: 273 sheet: 0.11 (0.29), residues: 324 loop : -0.19 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.022 0.002 PHE A 207 TYR 0.014 0.001 TYR G 35 ARG 0.006 0.000 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 7) link_NAG-ASN : angle 2.42098 ( 21) link_BETA1-4 : bond 0.00213 ( 5) link_BETA1-4 : angle 2.12759 ( 15) hydrogen bonds : bond 0.03427 ( 426) hydrogen bonds : angle 5.01313 ( 1227) SS BOND : bond 0.00330 ( 11) SS BOND : angle 0.77348 ( 22) covalent geometry : bond 0.00335 ( 9121) covalent geometry : angle 0.57032 (12383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8264 (mmt180) REVERT: E 141 MET cc_start: 0.8434 (ttt) cc_final: 0.8059 (ttp) REVERT: E 236 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6602 (mp0) REVERT: E 409 LEU cc_start: 0.8236 (tp) cc_final: 0.8015 (tt) REVERT: G 32 LEU cc_start: 0.7328 (mt) cc_final: 0.6898 (mt) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 0.9093 time to fit residues: 101.1620 Evaluate side-chains 95 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 71 optimal weight: 0.0670 chunk 61 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 109 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138879 restraints weight = 10226.892| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.17 r_work: 0.3377 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9144 Z= 0.110 Angle : 0.545 9.994 12441 Z= 0.280 Chirality : 0.043 0.145 1452 Planarity : 0.004 0.055 1519 Dihedral : 7.787 70.842 1504 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.92 % Allowed : 16.15 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.40 (0.26), residues: 1065 helix: 1.27 (0.30), residues: 274 sheet: 0.34 (0.29), residues: 331 loop : -0.31 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS F 295 PHE 0.027 0.002 PHE B 108 TYR 0.021 0.001 TYR B 100 ARG 0.006 0.000 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 7) link_NAG-ASN : angle 2.20414 ( 21) link_BETA1-4 : bond 0.00311 ( 5) link_BETA1-4 : angle 2.01286 ( 15) hydrogen bonds : bond 0.03297 ( 426) hydrogen bonds : angle 4.84947 ( 1227) SS BOND : bond 0.00245 ( 11) SS BOND : angle 0.61378 ( 22) covalent geometry : bond 0.00241 ( 9121) covalent geometry : angle 0.53354 (12383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8680 (p) cc_final: 0.8382 (t) REVERT: A 204 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8079 (tp40) REVERT: E 122 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7638 (mt0) REVERT: E 141 MET cc_start: 0.8348 (ttt) cc_final: 0.7766 (ttp) REVERT: E 144 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.6705 (ptp-110) REVERT: E 236 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6450 (mp0) REVERT: F 279 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7126 (mmtt) REVERT: G 32 LEU cc_start: 0.7537 (mt) cc_final: 0.7120 (mt) outliers start: 19 outliers final: 8 residues processed: 111 average time/residue: 0.9177 time to fit residues: 112.6490 Evaluate side-chains 89 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN E 138 HIS E 153 ASN E 223 ASN E 337 GLN ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128537 restraints weight = 10361.474| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.30 r_work: 0.3326 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9144 Z= 0.287 Angle : 0.677 11.043 12441 Z= 0.343 Chirality : 0.048 0.163 1452 Planarity : 0.005 0.053 1519 Dihedral : 8.883 74.326 1504 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.62 % Allowed : 16.65 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.18 (0.25), residues: 1065 helix: 0.97 (0.30), residues: 284 sheet: 0.08 (0.28), residues: 317 loop : -0.25 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.006 0.002 HIS A 173 PHE 0.025 0.003 PHE E 117 TYR 0.019 0.002 TYR G 35 ARG 0.006 0.001 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 7) link_NAG-ASN : angle 2.65549 ( 21) link_BETA1-4 : bond 0.00268 ( 5) link_BETA1-4 : angle 2.39182 ( 15) hydrogen bonds : bond 0.03813 ( 426) hydrogen bonds : angle 5.08508 ( 1227) SS BOND : bond 0.00636 ( 11) SS BOND : angle 1.05629 ( 22) covalent geometry : bond 0.00679 ( 9121) covalent geometry : angle 0.66252 (12383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.042 Fit side-chains REVERT: E 141 MET cc_start: 0.8620 (ttt) cc_final: 0.8270 (ttp) REVERT: E 236 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6740 (mp0) REVERT: E 338 ASN cc_start: 0.8325 (t0) cc_final: 0.8052 (t0) REVERT: F 185 LYS cc_start: 0.7075 (tttp) cc_final: 0.6562 (tttm) REVERT: F 279 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7134 (mmtt) REVERT: F 338 ASN cc_start: 0.8746 (t0) cc_final: 0.8456 (t0) outliers start: 26 outliers final: 13 residues processed: 117 average time/residue: 0.9979 time to fit residues: 127.7080 Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131023 restraints weight = 10417.967| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.35 r_work: 0.3225 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9144 Z= 0.171 Angle : 0.601 11.117 12441 Z= 0.307 Chirality : 0.045 0.141 1452 Planarity : 0.004 0.050 1519 Dihedral : 8.471 72.779 1504 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 18.37 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.25 (0.25), residues: 1065 helix: 1.13 (0.30), residues: 278 sheet: 0.08 (0.28), residues: 317 loop : -0.23 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 PHE 0.022 0.002 PHE A 207 TYR 0.014 0.002 TYR G 35 ARG 0.008 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 7) link_NAG-ASN : angle 2.50770 ( 21) link_BETA1-4 : bond 0.00206 ( 5) link_BETA1-4 : angle 2.09264 ( 15) hydrogen bonds : bond 0.03521 ( 426) hydrogen bonds : angle 5.00487 ( 1227) SS BOND : bond 0.00385 ( 11) SS BOND : angle 0.78112 ( 22) covalent geometry : bond 0.00396 ( 9121) covalent geometry : angle 0.58856 (12383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: E 141 MET cc_start: 0.8478 (ttt) cc_final: 0.7865 (ttp) REVERT: E 144 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6599 (ptp-110) REVERT: E 236 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6630 (mp0) REVERT: E 298 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (ptpt) REVERT: E 338 ASN cc_start: 0.8348 (t0) cc_final: 0.8097 (t0) REVERT: F 185 LYS cc_start: 0.6920 (tttp) cc_final: 0.6419 (tttm) REVERT: F 279 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.6941 (mmtt) REVERT: F 338 ASN cc_start: 0.8719 (t0) cc_final: 0.8369 (t0) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.8866 time to fit residues: 101.5586 Evaluate side-chains 102 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132444 restraints weight = 10319.296| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.23 r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9144 Z= 0.161 Angle : 0.586 9.236 12441 Z= 0.300 Chirality : 0.045 0.141 1452 Planarity : 0.004 0.051 1519 Dihedral : 8.197 72.327 1504 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.22 % Allowed : 17.96 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.31 (0.25), residues: 1065 helix: 1.28 (0.30), residues: 277 sheet: 0.02 (0.28), residues: 324 loop : -0.18 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.020 0.002 PHE E 117 TYR 0.018 0.002 TYR B 100 ARG 0.008 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 7) link_NAG-ASN : angle 2.41717 ( 21) link_BETA1-4 : bond 0.00187 ( 5) link_BETA1-4 : angle 2.11117 ( 15) hydrogen bonds : bond 0.03489 ( 426) hydrogen bonds : angle 4.93132 ( 1227) SS BOND : bond 0.00367 ( 11) SS BOND : angle 0.73413 ( 22) covalent geometry : bond 0.00373 ( 9121) covalent geometry : angle 0.57350 (12383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: E 141 MET cc_start: 0.8463 (ttt) cc_final: 0.7854 (ttp) REVERT: E 144 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.6618 (ptp-110) REVERT: E 236 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6607 (mp0) REVERT: E 338 ASN cc_start: 0.8353 (t0) cc_final: 0.8104 (t0) REVERT: F 185 LYS cc_start: 0.6924 (tttp) cc_final: 0.6428 (tttm) REVERT: F 279 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6923 (mmtt) REVERT: F 338 ASN cc_start: 0.8712 (t0) cc_final: 0.8331 (t0) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.7987 time to fit residues: 91.9772 Evaluate side-chains 103 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 368 TYR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138475 restraints weight = 10238.916| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.16 r_work: 0.3374 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9144 Z= 0.122 Angle : 0.560 10.011 12441 Z= 0.288 Chirality : 0.044 0.145 1452 Planarity : 0.004 0.053 1519 Dihedral : 7.681 71.309 1504 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 18.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.50 (0.26), residues: 1065 helix: 1.44 (0.30), residues: 277 sheet: 0.14 (0.28), residues: 324 loop : -0.09 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 PHE 0.018 0.002 PHE A 207 TYR 0.017 0.002 TYR C 43 ARG 0.011 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 7) link_NAG-ASN : angle 2.23938 ( 21) link_BETA1-4 : bond 0.00305 ( 5) link_BETA1-4 : angle 2.01667 ( 15) hydrogen bonds : bond 0.03320 ( 426) hydrogen bonds : angle 4.82821 ( 1227) SS BOND : bond 0.00365 ( 11) SS BOND : angle 0.65108 ( 22) covalent geometry : bond 0.00271 ( 9121) covalent geometry : angle 0.54883 (12383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8429 (t) REVERT: E 141 MET cc_start: 0.8428 (ttt) cc_final: 0.7856 (ttp) REVERT: E 144 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.6703 (ptp-110) REVERT: E 236 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6499 (mp0) REVERT: F 185 LYS cc_start: 0.6967 (tttp) cc_final: 0.6484 (tttm) REVERT: F 279 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6992 (mmtt) REVERT: F 338 ASN cc_start: 0.8689 (t0) cc_final: 0.8365 (t0) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.8304 time to fit residues: 92.5567 Evaluate side-chains 93 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 0.0170 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 138 HIS E 153 ASN E 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.174288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135107 restraints weight = 10326.519| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.31 r_work: 0.3404 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.130 Angle : 0.565 9.754 12441 Z= 0.289 Chirality : 0.044 0.143 1452 Planarity : 0.004 0.054 1519 Dihedral : 7.599 70.949 1504 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.72 % Allowed : 18.77 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.57 (0.26), residues: 1065 helix: 1.55 (0.30), residues: 277 sheet: 0.30 (0.28), residues: 331 loop : -0.19 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 PHE 0.018 0.002 PHE E 117 TYR 0.014 0.001 TYR B 100 ARG 0.008 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 7) link_NAG-ASN : angle 2.22158 ( 21) link_BETA1-4 : bond 0.00236 ( 5) link_BETA1-4 : angle 2.03607 ( 15) hydrogen bonds : bond 0.03375 ( 426) hydrogen bonds : angle 4.76203 ( 1227) SS BOND : bond 0.00369 ( 11) SS BOND : angle 0.70875 ( 22) covalent geometry : bond 0.00293 ( 9121) covalent geometry : angle 0.55396 (12383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7133.59 seconds wall clock time: 122 minutes 42.08 seconds (7362.08 seconds total)