Starting phenix.real_space_refine on Mon Mar 11 03:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/03_2024/8eq4_28535_updated.pdb" } resolution = 2.71 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= 0.003 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 33 5.16 5 C 4485 2.51 5 N 1119 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6903 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2217 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2217 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2217 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.16, per 1000 atoms: 0.60 Number of scatterers: 6903 At special positions: 0 Unit cell: (80.122, 81.774, 124.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 3 15.00 O 1263 8.00 N 1119 7.00 C 4485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 9 sheets defined 34.6% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 58 through 95 removed outlier: 3.775A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.191A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 338 removed outlier: 3.536A pdb=" N LYS A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 95 removed outlier: 3.775A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 273 through 277 removed outlier: 4.191A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 303 through 338 removed outlier: 3.536A pdb=" N LYS B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 95 removed outlier: 3.774A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 273 through 277 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 303 through 338 removed outlier: 3.536A pdb=" N LYS C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 101 through 107 removed outlier: 8.379A pdb=" N PHE A 291 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 244 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP A 297 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 241 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 233 removed outlier: 3.619A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 115 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 242 removed outlier: 8.819A pdb=" N THR A 238 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE A 282 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 240 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 284 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET A 242 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU A 286 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP A 287 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A 181 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 127 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG A 188 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 125 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 101 through 107 removed outlier: 8.379A pdb=" N PHE B 291 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 244 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP B 297 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 241 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 233 removed outlier: 3.619A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 115 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 237 through 242 removed outlier: 8.819A pdb=" N THR B 238 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE B 282 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL B 240 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 284 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET B 242 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 286 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP B 287 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU B 181 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 127 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG B 188 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU B 125 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 101 through 107 removed outlier: 8.379A pdb=" N PHE C 291 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU C 244 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP C 297 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 241 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 229 through 233 removed outlier: 3.618A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 115 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 237 through 242 removed outlier: 8.819A pdb=" N THR C 238 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE C 282 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL C 240 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL C 284 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET C 242 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU C 286 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP C 287 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU C 181 " --> pdb=" O TRP C 287 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 127 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG C 188 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C 125 " --> pdb=" O ARG C 188 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1080 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: 2.10 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1082 1.32 - 1.44: 1986 1.44 - 1.56: 3946 1.56 - 1.69: 6 1.69 - 1.81: 51 Bond restraints: 7071 Sorted by residual: bond pdb=" O1 PIO C 405 " pdb=" P1 PIO C 405 " ideal model delta sigma weight residual 1.648 1.478 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" O1 PIO B 405 " pdb=" P1 PIO B 405 " ideal model delta sigma weight residual 1.648 1.478 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" O1 PIO A 405 " pdb=" P1 PIO A 405 " ideal model delta sigma weight residual 1.648 1.479 0.169 2.00e-02 2.50e+03 7.18e+01 bond pdb=" C1B PIO B 405 " pdb=" O3C PIO B 405 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1B PIO A 405 " pdb=" O3C PIO A 405 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 7066 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 242 107.23 - 113.92: 3978 113.92 - 120.60: 2739 120.60 - 127.29: 2548 127.29 - 133.97: 78 Bond angle restraints: 9585 Sorted by residual: angle pdb=" C ARG B 93 " pdb=" CA ARG B 93 " pdb=" CB ARG B 93 " ideal model delta sigma weight residual 110.90 104.03 6.87 1.58e+00 4.01e-01 1.89e+01 angle pdb=" C ARG C 93 " pdb=" CA ARG C 93 " pdb=" CB ARG C 93 " ideal model delta sigma weight residual 110.90 104.04 6.86 1.58e+00 4.01e-01 1.89e+01 angle pdb=" C ARG A 93 " pdb=" CA ARG A 93 " pdb=" CB ARG A 93 " ideal model delta sigma weight residual 110.90 104.08 6.82 1.58e+00 4.01e-01 1.87e+01 angle pdb=" N TYR B 227 " pdb=" CA TYR B 227 " pdb=" C TYR B 227 " ideal model delta sigma weight residual 109.62 115.44 -5.82 1.50e+00 4.44e-01 1.50e+01 angle pdb=" N TYR A 227 " pdb=" CA TYR A 227 " pdb=" C TYR A 227 " ideal model delta sigma weight residual 109.62 115.43 -5.81 1.50e+00 4.44e-01 1.50e+01 ... (remaining 9580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 4113 23.00 - 45.99: 195 45.99 - 68.99: 30 68.99 - 91.99: 9 91.99 - 114.99: 24 Dihedral angle restraints: 4371 sinusoidal: 1857 harmonic: 2514 Sorted by residual: dihedral pdb=" N2 NAG A 404 " pdb=" C2 NAG A 404 " pdb=" C3 NAG A 404 " pdb=" O3 NAG A 404 " ideal model delta sinusoidal sigma weight residual 62.25 177.24 -114.99 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" N2 NAG B 404 " pdb=" C2 NAG B 404 " pdb=" C3 NAG B 404 " pdb=" O3 NAG B 404 " ideal model delta sinusoidal sigma weight residual 62.25 177.24 -114.99 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" N2 NAG C 404 " pdb=" C2 NAG C 404 " pdb=" C3 NAG C 404 " pdb=" O3 NAG C 404 " ideal model delta sinusoidal sigma weight residual 62.25 177.18 -114.93 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 4368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 937 0.058 - 0.116: 146 0.116 - 0.175: 9 0.175 - 0.233: 0 0.233 - 0.291: 6 Chirality restraints: 1098 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 148 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1095 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " 0.304 2.00e-02 2.50e+03 2.57e-01 8.29e+02 pdb=" C7 NAG A 403 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.304 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C7 NAG C 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 403 " -0.303 2.00e-02 2.50e+03 2.57e-01 8.27e+02 pdb=" C7 NAG B 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 403 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 403 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG B 403 " -0.035 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1095 2.77 - 3.30: 6616 3.30 - 3.83: 11171 3.83 - 4.37: 12817 4.37 - 4.90: 22866 Nonbonded interactions: 54565 Sorted by model distance: nonbonded pdb=" OH TYR B 119 " pdb=" OE2 GLU B 224 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR A 119 " pdb=" OE2 GLU A 224 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR C 119 " pdb=" OE2 GLU C 224 " model vdw 2.233 2.440 nonbonded pdb=" ND2 ASN C 302 " pdb=" OD1 ASN C 305 " model vdw 2.363 2.520 nonbonded pdb=" ND2 ASN A 302 " pdb=" OD1 ASN A 305 " model vdw 2.364 2.520 ... (remaining 54560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.800 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.370 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.006 0.170 7071 Z= 0.419 Angle : 0.735 10.089 9585 Z= 0.324 Chirality : 0.047 0.291 1098 Planarity : 0.020 0.257 1191 Dihedral : 16.443 114.987 2724 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 843 helix: 3.09 (0.26), residues: 315 sheet: -0.31 (0.29), residues: 330 loop : -0.66 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 330 HIS 0.003 0.001 HIS A 131 PHE 0.011 0.001 PHE A 204 TYR 0.008 0.001 TYR C 86 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.804 Fit side-chains REVERT: A 92 PHE cc_start: 0.8211 (t80) cc_final: 0.7891 (t80) REVERT: A 326 LEU cc_start: 0.8347 (tt) cc_final: 0.8010 (tt) REVERT: B 92 PHE cc_start: 0.8231 (t80) cc_final: 0.8028 (t80) REVERT: B 326 LEU cc_start: 0.8341 (tt) cc_final: 0.8014 (tt) REVERT: C 76 LEU cc_start: 0.8776 (tp) cc_final: 0.8574 (mp) REVERT: C 92 PHE cc_start: 0.8201 (t80) cc_final: 0.7998 (t80) REVERT: C 158 ASP cc_start: 0.8752 (t0) cc_final: 0.8529 (t0) REVERT: C 326 LEU cc_start: 0.8332 (tt) cc_final: 0.8003 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 1.1640 time to fit residues: 183.2567 Evaluate side-chains 88 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 302 ASN A 305 ASN C 131 HIS C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7071 Z= 0.232 Angle : 0.588 8.699 9585 Z= 0.285 Chirality : 0.047 0.298 1098 Planarity : 0.003 0.024 1191 Dihedral : 14.657 92.451 1215 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.88 % Allowed : 11.54 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 843 helix: 2.94 (0.26), residues: 315 sheet: -0.08 (0.28), residues: 318 loop : -0.50 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.001 0.001 HIS B 131 PHE 0.016 0.001 PHE C 204 TYR 0.014 0.001 TYR A 86 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.853 Fit side-chains REVERT: A 92 PHE cc_start: 0.8239 (t80) cc_final: 0.7932 (t80) REVERT: B 92 PHE cc_start: 0.8251 (t80) cc_final: 0.7900 (t80) REVERT: B 176 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: C 92 PHE cc_start: 0.8198 (t80) cc_final: 0.7829 (t80) outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.6801 time to fit residues: 76.7494 Evaluate side-chains 95 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 325 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7071 Z= 0.192 Angle : 0.558 6.817 9585 Z= 0.264 Chirality : 0.047 0.294 1098 Planarity : 0.003 0.024 1191 Dihedral : 12.008 74.090 1215 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.02 % Allowed : 12.12 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 843 helix: 2.96 (0.27), residues: 315 sheet: -0.12 (0.28), residues: 312 loop : -0.31 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.001 0.000 HIS B 131 PHE 0.024 0.001 PHE C 83 TYR 0.008 0.001 TYR B 74 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 92 PHE cc_start: 0.8218 (t80) cc_final: 0.7887 (t80) REVERT: B 92 PHE cc_start: 0.8207 (t80) cc_final: 0.7870 (t80) REVERT: C 92 PHE cc_start: 0.8170 (t80) cc_final: 0.7814 (t80) outliers start: 14 outliers final: 3 residues processed: 102 average time/residue: 0.6604 time to fit residues: 74.2493 Evaluate side-chains 90 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain C residue 155 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7071 Z= 0.170 Angle : 0.571 9.079 9585 Z= 0.261 Chirality : 0.047 0.300 1098 Planarity : 0.003 0.023 1191 Dihedral : 10.307 59.708 1215 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.02 % Allowed : 12.84 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 843 helix: 2.99 (0.27), residues: 315 sheet: -0.14 (0.28), residues: 312 loop : -0.36 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 304 HIS 0.001 0.000 HIS B 131 PHE 0.015 0.001 PHE A 204 TYR 0.014 0.001 TYR C 227 ARG 0.001 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 92 PHE cc_start: 0.8205 (t80) cc_final: 0.7882 (t80) REVERT: B 92 PHE cc_start: 0.8207 (t80) cc_final: 0.7868 (t80) REVERT: B 176 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: C 92 PHE cc_start: 0.8189 (t80) cc_final: 0.7822 (t80) REVERT: C 176 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8542 (mm-30) outliers start: 14 outliers final: 6 residues processed: 100 average time/residue: 0.6175 time to fit residues: 69.5317 Evaluate side-chains 95 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7071 Z= 0.179 Angle : 0.550 7.621 9585 Z= 0.254 Chirality : 0.046 0.303 1098 Planarity : 0.003 0.023 1191 Dihedral : 9.396 59.387 1215 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.02 % Allowed : 13.85 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 843 helix: 3.07 (0.27), residues: 315 sheet: -0.12 (0.28), residues: 312 loop : -0.31 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.001 0.000 HIS B 131 PHE 0.030 0.001 PHE C 83 TYR 0.015 0.001 TYR C 227 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 92 PHE cc_start: 0.8210 (t80) cc_final: 0.7883 (t80) REVERT: B 92 PHE cc_start: 0.8195 (t80) cc_final: 0.7835 (t80) REVERT: B 158 ASP cc_start: 0.8651 (t0) cc_final: 0.8403 (t0) REVERT: C 92 PHE cc_start: 0.8184 (t80) cc_final: 0.7830 (t80) REVERT: C 176 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (mm-30) outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 0.5190 time to fit residues: 56.4155 Evaluate side-chains 93 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 176 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7071 Z= 0.231 Angle : 0.582 8.530 9585 Z= 0.267 Chirality : 0.047 0.309 1098 Planarity : 0.002 0.022 1191 Dihedral : 8.808 59.417 1215 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.32 % Allowed : 13.13 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 843 helix: 3.07 (0.27), residues: 315 sheet: -0.15 (0.28), residues: 312 loop : -0.24 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 304 HIS 0.001 0.000 HIS B 131 PHE 0.014 0.001 PHE A 204 TYR 0.013 0.001 TYR C 227 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 92 PHE cc_start: 0.8230 (t80) cc_final: 0.7895 (t80) REVERT: B 92 PHE cc_start: 0.8198 (t80) cc_final: 0.7816 (t80) REVERT: B 158 ASP cc_start: 0.8691 (t0) cc_final: 0.8464 (t0) REVERT: B 176 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: C 92 PHE cc_start: 0.8141 (t80) cc_final: 0.7824 (t80) REVERT: C 176 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8390 (mm-30) outliers start: 23 outliers final: 10 residues processed: 104 average time/residue: 0.5424 time to fit residues: 63.4114 Evaluate side-chains 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 195 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7071 Z= 0.184 Angle : 0.563 8.612 9585 Z= 0.261 Chirality : 0.046 0.306 1098 Planarity : 0.002 0.022 1191 Dihedral : 8.501 59.165 1215 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 14.29 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 843 helix: 3.11 (0.27), residues: 315 sheet: -0.18 (0.28), residues: 312 loop : -0.24 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.001 0.000 HIS B 130 PHE 0.030 0.001 PHE C 83 TYR 0.014 0.001 TYR C 227 ARG 0.001 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 92 PHE cc_start: 0.8230 (t80) cc_final: 0.7899 (t80) REVERT: B 92 PHE cc_start: 0.8199 (t80) cc_final: 0.7824 (t80) REVERT: B 158 ASP cc_start: 0.8706 (t0) cc_final: 0.8480 (t0) REVERT: B 176 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: C 92 PHE cc_start: 0.8140 (t80) cc_final: 0.7827 (t80) REVERT: C 176 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8399 (mm-30) outliers start: 19 outliers final: 9 residues processed: 100 average time/residue: 0.5335 time to fit residues: 59.9507 Evaluate side-chains 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 176 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7071 Z= 0.181 Angle : 0.598 9.489 9585 Z= 0.272 Chirality : 0.046 0.309 1098 Planarity : 0.002 0.022 1191 Dihedral : 8.234 58.605 1215 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.45 % Allowed : 14.43 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 843 helix: 3.04 (0.27), residues: 318 sheet: -0.15 (0.28), residues: 312 loop : -0.21 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 304 HIS 0.001 0.000 HIS C 131 PHE 0.014 0.001 PHE B 204 TYR 0.014 0.001 TYR C 227 ARG 0.001 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 92 PHE cc_start: 0.8229 (t80) cc_final: 0.7932 (t80) REVERT: B 92 PHE cc_start: 0.8183 (t80) cc_final: 0.7812 (t80) REVERT: B 158 ASP cc_start: 0.8688 (t0) cc_final: 0.8456 (t0) REVERT: B 176 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: C 92 PHE cc_start: 0.8145 (t80) cc_final: 0.7836 (t80) REVERT: C 176 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8389 (mm-30) outliers start: 17 outliers final: 10 residues processed: 101 average time/residue: 0.5832 time to fit residues: 65.8858 Evaluate side-chains 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 176 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 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 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7071 Z= 0.170 Angle : 0.570 10.381 9585 Z= 0.264 Chirality : 0.046 0.308 1098 Planarity : 0.003 0.022 1191 Dihedral : 7.982 58.062 1215 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.88 % Allowed : 15.58 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 843 helix: 3.00 (0.27), residues: 318 sheet: -0.12 (0.28), residues: 312 loop : -0.22 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 304 HIS 0.001 0.000 HIS C 131 PHE 0.033 0.001 PHE C 83 TYR 0.014 0.001 TYR C 227 ARG 0.001 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 92 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80) REVERT: A 223 CYS cc_start: 0.8739 (m) cc_final: 0.8348 (m) REVERT: B 92 PHE cc_start: 0.8180 (t80) cc_final: 0.7802 (t80) REVERT: B 158 ASP cc_start: 0.8696 (t0) cc_final: 0.8447 (t0) REVERT: B 176 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8472 (mm-30) REVERT: C 73 ILE cc_start: 0.8834 (tt) cc_final: 0.8634 (pp) REVERT: C 92 PHE cc_start: 0.8107 (t80) cc_final: 0.7795 (t80) outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 0.5185 time to fit residues: 56.7454 Evaluate side-chains 96 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 155 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7071 Z= 0.290 Angle : 0.630 11.328 9585 Z= 0.292 Chirality : 0.047 0.319 1098 Planarity : 0.003 0.022 1191 Dihedral : 7.891 59.041 1215 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.88 % Allowed : 16.02 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 843 helix: 2.93 (0.27), residues: 318 sheet: -0.23 (0.28), residues: 312 loop : -0.13 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 304 HIS 0.001 0.000 HIS C 98 PHE 0.014 0.001 PHE B 232 TYR 0.017 0.001 TYR B 74 ARG 0.003 0.000 ARG A 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 92 PHE cc_start: 0.8225 (t80) cc_final: 0.7945 (t80) REVERT: B 92 PHE cc_start: 0.8205 (t80) cc_final: 0.7805 (t80) REVERT: B 158 ASP cc_start: 0.8697 (t0) cc_final: 0.8487 (t0) REVERT: B 176 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: C 92 PHE cc_start: 0.8114 (t80) cc_final: 0.7775 (t80) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.5919 time to fit residues: 64.2411 Evaluate side-chains 98 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0870 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.064130 restraints weight = 13680.686| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.26 r_work: 0.2715 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7071 Z= 0.312 Angle : 0.606 11.262 9585 Z= 0.289 Chirality : 0.047 0.313 1098 Planarity : 0.003 0.022 1191 Dihedral : 7.813 59.837 1215 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.73 % Allowed : 16.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 843 helix: 2.88 (0.27), residues: 318 sheet: -0.31 (0.28), residues: 312 loop : -0.03 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.001 0.000 HIS C 131 PHE 0.036 0.002 PHE C 83 TYR 0.011 0.001 TYR A 74 ARG 0.003 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.00 seconds wall clock time: 42 minutes 7.21 seconds (2527.21 seconds total)