Starting phenix.real_space_refine on Wed Sep 17 13:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y81_39029/09_2025/8y81_39029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y81_39029/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y81_39029/09_2025/8y81_39029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y81_39029/09_2025/8y81_39029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y81_39029/09_2025/8y81_39029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y81_39029/09_2025/8y81_39029.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.25, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 333.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.47 Time building geometry restraints manager: 1.22 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: 2.300 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG E 144 TYR 0.059 0.003 TYR A 154 PHE 0.036 0.003 PHE E 117 TRP 0.018 0.002 TRP B 103 HIS 0.011 0.002 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 9121) covalent geometry : angle 0.99699 (12383) SS BOND : bond 0.00649 ( 11) SS BOND : angle 1.56101 ( 22) hydrogen bonds : bond 0.12190 ( 426) hydrogen bonds : angle 7.26437 ( 1227) link_BETA1-4 : bond 0.00431 ( 5) link_BETA1-4 : angle 1.98245 ( 15) link_NAG-ASN : bond 0.00904 ( 7) link_NAG-ASN : angle 4.16850 ( 21) *********************** 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 : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.4959 time to fit residues: 67.0665 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 : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 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: B 134 ASN B 151 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 174 GLN E 350 GLN F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.170998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133050 restraints weight = 10380.156| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.23 r_work: 0.3258 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9144 Z= 0.177 Angle : 0.657 10.185 12441 Z= 0.338 Chirality : 0.046 0.162 1452 Planarity : 0.005 0.062 1519 Dihedral : 11.090 75.871 1504 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.82 % Allowed : 8.27 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.24), residues: 1065 helix: -0.35 (0.28), residues: 282 sheet: -0.04 (0.29), residues: 326 loop : -0.48 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 330 TYR 0.018 0.002 TYR G 35 PHE 0.020 0.002 PHE E 117 TRP 0.013 0.001 TRP A 222 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9121) covalent geometry : angle 0.64112 (12383) SS BOND : bond 0.00406 ( 11) SS BOND : angle 0.91665 ( 22) hydrogen bonds : bond 0.03975 ( 426) hydrogen bonds : angle 5.63747 ( 1227) link_BETA1-4 : bond 0.00190 ( 5) link_BETA1-4 : angle 2.18116 ( 15) link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 3.06371 ( 21) *********************** 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 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8324 (ttp-170) REVERT: E 141 MET cc_start: 0.8367 (ttt) cc_final: 0.8043 (ttp) REVERT: E 372 ASN cc_start: 0.6336 (t0) cc_final: 0.6110 (t0) REVERT: G 32 LEU cc_start: 0.7444 (mt) cc_final: 0.7232 (mt) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 0.4354 time to fit residues: 47.3096 Evaluate side-chains 93 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain C residue 32 LEU 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 343 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 223 ASN E 393 GLN F 118 HIS F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129998 restraints weight = 10255.768| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.29 r_work: 0.3363 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9144 Z= 0.210 Angle : 0.647 11.096 12441 Z= 0.332 Chirality : 0.047 0.151 1452 Planarity : 0.005 0.055 1519 Dihedral : 10.050 75.936 1504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.32 % Allowed : 11.10 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.25), residues: 1065 helix: 0.26 (0.29), residues: 277 sheet: -0.08 (0.28), residues: 322 loop : -0.37 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 374 TYR 0.019 0.002 TYR G 35 PHE 0.020 0.002 PHE E 117 TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9121) covalent geometry : angle 0.63243 (12383) SS BOND : bond 0.00459 ( 11) SS BOND : angle 0.94974 ( 22) hydrogen bonds : bond 0.03785 ( 426) hydrogen bonds : angle 5.34275 ( 1227) link_BETA1-4 : bond 0.00167 ( 5) link_BETA1-4 : angle 2.21827 ( 15) link_NAG-ASN : bond 0.00501 ( 7) link_NAG-ASN : angle 2.81721 ( 21) *********************** 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 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.351 Fit side-chains REVERT: A 129 ARG cc_start: 0.8625 (ttp-170) cc_final: 0.8321 (ttp-170) REVERT: E 141 MET cc_start: 0.8470 (ttt) cc_final: 0.8131 (ttp) REVERT: E 372 ASN cc_start: 0.6417 (t0) cc_final: 0.6183 (t0) REVERT: F 185 LYS cc_start: 0.7212 (tttp) cc_final: 0.6858 (tttm) REVERT: F 401 GLU cc_start: 0.8200 (pt0) cc_final: 0.7891 (pt0) REVERT: G 32 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7332 (mp) outliers start: 23 outliers final: 12 residues processed: 114 average time/residue: 0.4644 time to fit residues: 57.2486 Evaluate side-chains 105 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 C residue 32 LEU 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 369 ASN Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.0010 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 174 GLN E 223 ASN 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 = 0.3890 r_free = 0.3890 target = 0.172709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133367 restraints weight = 10381.304| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.31 r_work: 0.3253 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9144 Z= 0.137 Angle : 0.590 10.319 12441 Z= 0.302 Chirality : 0.045 0.163 1452 Planarity : 0.004 0.056 1519 Dihedral : 8.997 73.590 1504 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.12 % Allowed : 13.22 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1065 helix: 0.67 (0.29), residues: 273 sheet: 0.00 (0.29), residues: 322 loop : -0.30 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 144 TYR 0.013 0.001 TYR G 35 PHE 0.017 0.002 PHE A 207 TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9121) covalent geometry : angle 0.57658 (12383) SS BOND : bond 0.00300 ( 11) SS BOND : angle 0.73531 ( 22) hydrogen bonds : bond 0.03487 ( 426) hydrogen bonds : angle 5.12746 ( 1227) link_BETA1-4 : bond 0.00246 ( 5) link_BETA1-4 : angle 2.05751 ( 15) link_NAG-ASN : bond 0.00337 ( 7) link_NAG-ASN : angle 2.55104 ( 21) *********************** 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 108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8130 (mmt180) REVERT: E 141 MET cc_start: 0.8445 (ttt) cc_final: 0.8077 (ttp) REVERT: E 409 LEU cc_start: 0.8257 (tp) cc_final: 0.8031 (tt) REVERT: F 401 GLU cc_start: 0.8185 (pt0) cc_final: 0.7803 (pt0) REVERT: G 32 LEU cc_start: 0.7468 (mt) cc_final: 0.7077 (mt) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 0.4115 time to fit residues: 44.6527 Evaluate side-chains 94 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 32 LEU 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 104 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3891 r_free = 0.3891 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133696 restraints weight = 10318.085| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.24 r_work: 0.3242 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9144 Z= 0.165 Angle : 0.593 10.521 12441 Z= 0.304 Chirality : 0.045 0.148 1452 Planarity : 0.004 0.053 1519 Dihedral : 8.670 73.573 1504 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.32 % Allowed : 15.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1065 helix: 0.80 (0.30), residues: 278 sheet: 0.01 (0.28), residues: 322 loop : -0.24 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 144 TYR 0.021 0.002 TYR B 100 PHE 0.019 0.002 PHE A 207 TRP 0.014 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9121) covalent geometry : angle 0.57961 (12383) SS BOND : bond 0.00360 ( 11) SS BOND : angle 0.82815 ( 22) hydrogen bonds : bond 0.03488 ( 426) hydrogen bonds : angle 5.07663 ( 1227) link_BETA1-4 : bond 0.00201 ( 5) link_BETA1-4 : angle 2.18247 ( 15) link_NAG-ASN : bond 0.00387 ( 7) link_NAG-ASN : angle 2.49545 ( 21) *********************** 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 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8443 (mmt180) cc_final: 0.8236 (mmt180) REVERT: E 141 MET cc_start: 0.8454 (ttt) cc_final: 0.8079 (ttp) REVERT: E 236 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6617 (mp0) REVERT: E 409 LEU cc_start: 0.8219 (tp) cc_final: 0.8014 (tt) REVERT: F 374 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8146 (mtt90) REVERT: F 401 GLU cc_start: 0.8169 (pt0) cc_final: 0.7948 (pt0) REVERT: G 32 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7012 (mt) outliers start: 23 outliers final: 12 residues processed: 105 average time/residue: 0.4067 time to fit residues: 46.4225 Evaluate side-chains 97 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 B residue 86 SER Chi-restraints excluded: chain B residue 156 SER 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 Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.170105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130418 restraints weight = 10337.482| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.29 r_work: 0.3331 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9144 Z= 0.199 Angle : 0.614 10.456 12441 Z= 0.315 Chirality : 0.046 0.145 1452 Planarity : 0.004 0.052 1519 Dihedral : 8.701 73.655 1504 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.93 % Allowed : 15.44 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.25), residues: 1065 helix: 0.88 (0.30), residues: 278 sheet: 0.04 (0.28), residues: 315 loop : -0.28 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 144 TYR 0.016 0.002 TYR G 35 PHE 0.019 0.002 PHE E 117 TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9121) covalent geometry : angle 0.60052 (12383) SS BOND : bond 0.00428 ( 11) SS BOND : angle 0.85890 ( 22) hydrogen bonds : bond 0.03575 ( 426) hydrogen bonds : angle 5.06214 ( 1227) link_BETA1-4 : bond 0.00174 ( 5) link_BETA1-4 : angle 2.24170 ( 15) link_NAG-ASN : bond 0.00463 ( 7) link_NAG-ASN : angle 2.56066 ( 21) *********************** 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 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 212 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (p) REVERT: E 141 MET cc_start: 0.8522 (ttt) cc_final: 0.8150 (ttp) REVERT: E 236 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6695 (mp0) REVERT: F 185 LYS cc_start: 0.7218 (tttp) cc_final: 0.6935 (tttt) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.3887 time to fit residues: 48.6001 Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 156 SER 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 E residue 253 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3886 r_free = 0.3886 target = 0.172043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133380 restraints weight = 10309.185| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.22 r_work: 0.3300 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9144 Z= 0.165 Angle : 0.596 10.283 12441 Z= 0.303 Chirality : 0.045 0.142 1452 Planarity : 0.004 0.052 1519 Dihedral : 8.403 73.081 1504 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.23 % Allowed : 15.94 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1065 helix: 0.96 (0.30), residues: 278 sheet: -0.04 (0.28), residues: 322 loop : -0.19 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 144 TYR 0.022 0.002 TYR B 100 PHE 0.018 0.002 PHE A 207 TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9121) covalent geometry : angle 0.58331 (12383) SS BOND : bond 0.00368 ( 11) SS BOND : angle 0.77905 ( 22) hydrogen bonds : bond 0.03481 ( 426) hydrogen bonds : angle 4.99868 ( 1227) link_BETA1-4 : bond 0.00233 ( 5) link_BETA1-4 : angle 2.14757 ( 15) link_NAG-ASN : bond 0.00389 ( 7) link_NAG-ASN : angle 2.47142 ( 21) *********************** 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: 32 poor density : 94 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: E 141 MET cc_start: 0.8446 (ttt) cc_final: 0.7854 (ttp) REVERT: E 144 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.6634 (ptp-110) REVERT: E 236 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6723 (mp0) REVERT: F 185 LYS cc_start: 0.7100 (tttp) cc_final: 0.6815 (tttt) REVERT: F 279 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.6952 (mmtt) REVERT: F 338 ASN cc_start: 0.8679 (t0) cc_final: 0.8370 (t0) outliers start: 32 outliers final: 19 residues processed: 109 average time/residue: 0.4192 time to fit residues: 49.8259 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 B residue 86 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 156 SER 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 413 ILE 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 Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.0030 chunk 64 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 overall best weight: 0.3288 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137719 restraints weight = 10317.457| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.22 r_work: 0.3356 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2032 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= 0.112 Angle : 0.554 9.802 12441 Z= 0.283 Chirality : 0.043 0.148 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.594 71.049 1504 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.02 % Allowed : 17.66 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1065 helix: 1.22 (0.30), residues: 278 sheet: 0.13 (0.28), residues: 324 loop : -0.10 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 144 TYR 0.013 0.001 TYR E 166 PHE 0.014 0.001 PHE F 376 TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9121) covalent geometry : angle 0.54216 (12383) SS BOND : bond 0.00236 ( 11) SS BOND : angle 0.62429 ( 22) hydrogen bonds : bond 0.03294 ( 426) hydrogen bonds : angle 4.78762 ( 1227) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 2.01260 ( 15) link_NAG-ASN : bond 0.00259 ( 7) link_NAG-ASN : angle 2.24026 ( 21) *********************** 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 108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.350 Fit side-chains REVERT: A 175 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8423 (t) REVERT: E 141 MET cc_start: 0.8352 (ttt) cc_final: 0.7774 (ttp) REVERT: E 144 ARG cc_start: 0.7331 (ttp-110) cc_final: 0.6717 (ptp-110) REVERT: E 236 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6487 (mp0) REVERT: F 185 LYS cc_start: 0.7095 (tttp) cc_final: 0.6626 (tttm) REVERT: F 279 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7094 (mmtt) REVERT: F 338 ASN cc_start: 0.8687 (t0) cc_final: 0.8351 (t0) outliers start: 20 outliers final: 11 residues processed: 101 average time/residue: 0.3873 time to fit residues: 43.1684 Evaluate side-chains 91 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 86 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 413 ILE 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 57 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 337 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133485 restraints weight = 10292.947| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.23 r_work: 0.3311 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9144 Z= 0.181 Angle : 0.601 10.503 12441 Z= 0.306 Chirality : 0.045 0.154 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.973 72.449 1504 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.42 % Allowed : 17.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1065 helix: 1.24 (0.30), residues: 278 sheet: 0.11 (0.28), residues: 324 loop : -0.13 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 144 TYR 0.022 0.002 TYR B 100 PHE 0.025 0.002 PHE B 108 TRP 0.018 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9121) covalent geometry : angle 0.58857 (12383) SS BOND : bond 0.00384 ( 11) SS BOND : angle 0.81551 ( 22) hydrogen bonds : bond 0.03534 ( 426) hydrogen bonds : angle 4.86529 ( 1227) link_BETA1-4 : bond 0.00176 ( 5) link_BETA1-4 : angle 2.21199 ( 15) link_NAG-ASN : bond 0.00422 ( 7) link_NAG-ASN : angle 2.40194 ( 21) *********************** 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 118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 148 ILE cc_start: 0.8511 (mm) cc_final: 0.8256 (mt) REVERT: E 141 MET cc_start: 0.8483 (ttt) cc_final: 0.7900 (ttp) REVERT: E 144 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.6645 (ptp-110) REVERT: E 236 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6572 (mp0) REVERT: F 185 LYS cc_start: 0.7115 (tttp) cc_final: 0.6634 (tttm) REVERT: F 279 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7003 (mmtt) REVERT: F 338 ASN cc_start: 0.8712 (t0) cc_final: 0.8354 (t0) outliers start: 24 outliers final: 15 residues processed: 106 average time/residue: 0.3767 time to fit residues: 44.0149 Evaluate side-chains 107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 86 SER Chi-restraints excluded: chain B residue 156 SER 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 413 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 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN ** F 109 HIS ** 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 = 0.3896 r_free = 0.3896 target = 0.173196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134549 restraints weight = 10291.461| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.23 r_work: 0.3329 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9144 Z= 0.153 Angle : 0.582 10.143 12441 Z= 0.297 Chirality : 0.045 0.152 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.874 72.119 1504 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.72 % Allowed : 18.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1065 helix: 1.31 (0.30), residues: 275 sheet: 0.13 (0.28), residues: 324 loop : -0.14 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 144 TYR 0.017 0.002 TYR B 100 PHE 0.023 0.002 PHE B 108 TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9121) covalent geometry : angle 0.56958 (12383) SS BOND : bond 0.00382 ( 11) SS BOND : angle 0.76995 ( 22) hydrogen bonds : bond 0.03458 ( 426) hydrogen bonds : angle 4.82155 ( 1227) link_BETA1-4 : bond 0.00206 ( 5) link_BETA1-4 : angle 2.08558 ( 15) link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.34913 ( 21) ********************** 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 103 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.271 Fit side-chains REVERT: A 129 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8226 (ttp-170) REVERT: A 175 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8499 (t) REVERT: E 141 MET cc_start: 0.8450 (ttt) cc_final: 0.7868 (ttp) REVERT: E 144 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6655 (ptp-110) REVERT: E 236 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6534 (mp0) REVERT: F 185 LYS cc_start: 0.7106 (tttp) cc_final: 0.6641 (tttm) REVERT: F 338 ASN cc_start: 0.8700 (t0) cc_final: 0.8362 (t0) outliers start: 17 outliers final: 14 residues processed: 96 average time/residue: 0.3609 time to fit residues: 38.3434 Evaluate side-chains 100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 86 SER Chi-restraints excluded: chain B residue 156 SER 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 413 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 149 THR 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 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 337 GLN ** F 109 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.175834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138221 restraints weight = 10170.238| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.15 r_work: 0.3327 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2157 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= 0.148 Angle : 0.573 10.102 12441 Z= 0.293 Chirality : 0.044 0.154 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.789 71.848 1504 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.32 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1065 helix: 1.36 (0.31), residues: 275 sheet: 0.15 (0.28), residues: 324 loop : -0.11 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 144 TYR 0.017 0.002 TYR C 43 PHE 0.023 0.002 PHE B 108 TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9121) covalent geometry : angle 0.56129 (12383) SS BOND : bond 0.00381 ( 11) SS BOND : angle 0.73036 ( 22) hydrogen bonds : bond 0.03411 ( 426) hydrogen bonds : angle 4.80078 ( 1227) link_BETA1-4 : bond 0.00206 ( 5) link_BETA1-4 : angle 2.07736 ( 15) link_NAG-ASN : bond 0.00352 ( 7) link_NAG-ASN : angle 2.31099 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.37 seconds wall clock time: 55 minutes 16.41 seconds (3316.41 seconds total)