Starting phenix.real_space_refine on Tue Nov 14 02:04:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_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_28535/11_2023/8eq4_28535_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_28535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eq4_28535/11_2023/8eq4_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-1.21rc1-5144/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: 10 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: 10 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: 10 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.03, per 1000 atoms: 0.58 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 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: 1.30 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: 2.14 Time building geometry restraints manager: 2.89 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 - 15.69: 3748 15.69 - 31.38: 284 31.38 - 47.07: 75 47.07 - 62.76: 3 62.76 - 78.45: 9 Dihedral angle restraints: 4119 sinusoidal: 1605 harmonic: 2514 Sorted by residual: dihedral pdb=" CA PHE A 204 " pdb=" C PHE A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA PHE C 204 " pdb=" C PHE C 204 " pdb=" N SER C 205 " pdb=" CA SER C 205 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CA PHE B 204 " pdb=" C PHE B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 ... (remaining 4116 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: 1.770 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: 5.810 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.200 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.110 ------------------------------------------------------------------------------- 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 : 12.356 78.450 2472 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 *********************** 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 : 0.744 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 1.0470 time to fit residues: 165.0133 Evaluate side-chains 84 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9652 ------------------------------------------------------------------------------- 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 302 ASN A 305 ASN C 131 HIS C 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7071 Z= 0.234 Angle : 0.566 8.461 9585 Z= 0.281 Chirality : 0.046 0.303 1098 Planarity : 0.003 0.024 1191 Dihedral : 7.339 53.087 963 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.88 % Allowed : 12.12 % Favored : 86.00 % 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: 3.04 (0.26), residues: 312 sheet: -0.07 (0.28), residues: 318 loop : -0.52 (0.41), residues: 213 *********************** 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 105 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.075 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 101 average time/residue: 0.6584 time to fit residues: 73.6442 Evaluate side-chains 91 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.2036 time to fit residues: 1.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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: 0.1794 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= 0.180 Angle : 0.525 6.122 9585 Z= 0.256 Chirality : 0.045 0.303 1098 Planarity : 0.003 0.023 1191 Dihedral : 7.366 54.954 963 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.02 % Allowed : 11.98 % Favored : 86.00 % 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: 2.97 (0.27), residues: 315 sheet: -0.12 (0.28), residues: 312 loop : -0.33 (0.41), residues: 216 *********************** 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 102 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 101 average time/residue: 0.7044 time to fit residues: 78.1007 Evaluate side-chains 88 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.2118 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= 0.215 Angle : 0.534 8.231 9585 Z= 0.256 Chirality : 0.045 0.309 1098 Planarity : 0.003 0.023 1191 Dihedral : 7.300 57.486 963 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.16 % Allowed : 12.84 % Favored : 84.99 % 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: 3.01 (0.27), residues: 315 sheet: -0.17 (0.28), residues: 312 loop : -0.34 (0.41), residues: 216 *********************** 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 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 0.5550 time to fit residues: 59.8394 Evaluate side-chains 89 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.0237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8510 moved from start: 0.2131 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= 0.180 Angle : 0.512 7.062 9585 Z= 0.247 Chirality : 0.045 0.308 1098 Planarity : 0.002 0.023 1191 Dihedral : 7.152 59.778 963 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.31 % Allowed : 13.42 % Favored : 84.27 % 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: 1.49 (0.29), residues: 843 helix: 3.06 (0.27), residues: 315 sheet: -0.15 (0.28), residues: 312 loop : -0.30 (0.41), residues: 216 *********************** 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 102 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 0.5420 time to fit residues: 59.9657 Evaluate side-chains 93 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1113 time to fit residues: 1.2331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.2357 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= 0.200 Angle : 0.534 8.328 9585 Z= 0.254 Chirality : 0.045 0.311 1098 Planarity : 0.002 0.023 1191 Dihedral : 7.078 57.942 963 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 13.71 % 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: 1.46 (0.29), residues: 843 helix: 3.04 (0.27), residues: 315 sheet: -0.18 (0.28), residues: 312 loop : -0.28 (0.41), residues: 216 *********************** 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 103 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.5041 time to fit residues: 56.2912 Evaluate side-chains 96 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.2120 time to fit residues: 2.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.2339 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= 0.175 Angle : 0.528 8.489 9585 Z= 0.251 Chirality : 0.045 0.309 1098 Planarity : 0.002 0.022 1191 Dihedral : 6.946 56.332 963 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.16 % Allowed : 14.29 % 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: 1.46 (0.29), residues: 843 helix: 3.01 (0.27), residues: 318 sheet: -0.23 (0.28), residues: 312 loop : -0.21 (0.41), residues: 213 *********************** 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 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.5268 time to fit residues: 58.2390 Evaluate side-chains 94 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1275 time to fit residues: 1.4173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.8506 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7071 Z= 0.162 Angle : 0.553 9.274 9585 Z= 0.258 Chirality : 0.044 0.312 1098 Planarity : 0.002 0.023 1191 Dihedral : 6.846 57.054 963 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.16 % Allowed : 14.43 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 843 helix: 3.01 (0.27), residues: 318 sheet: -0.19 (0.28), residues: 312 loop : -0.22 (0.41), residues: 213 *********************** 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 101 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.5096 time to fit residues: 56.5360 Evaluate side-chains 94 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1709 time to fit residues: 1.5600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8506 moved from start: 0.2433 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= 0.171 Angle : 0.550 10.601 9585 Z= 0.259 Chirality : 0.045 0.310 1098 Planarity : 0.002 0.023 1191 Dihedral : 6.791 57.583 963 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.88 % Allowed : 15.01 % 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: 1.46 (0.29), residues: 843 helix: 2.98 (0.27), residues: 318 sheet: -0.18 (0.28), residues: 312 loop : -0.24 (0.41), residues: 213 *********************** 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 97 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.5263 time to fit residues: 57.0253 Evaluate side-chains 91 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1134 time to fit residues: 1.2374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7071 Z= 0.233 Angle : 0.569 10.793 9585 Z= 0.268 Chirality : 0.046 0.314 1098 Planarity : 0.002 0.022 1191 Dihedral : 6.807 57.553 963 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 15.73 % Favored : 82.83 % 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: 2.88 (0.27), residues: 318 sheet: -0.21 (0.28), residues: 312 loop : -0.17 (0.41), residues: 213 ********************** 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 92 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 92 average time/residue: 0.5202 time to fit residues: 54.2126 Evaluate side-chains 89 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.0542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.090709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066034 restraints weight = 13624.695| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.24 r_work: 0.2778 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7071 Z= 0.204 Angle : 0.558 10.068 9585 Z= 0.265 Chirality : 0.046 0.314 1098 Planarity : 0.002 0.022 1191 Dihedral : 6.762 57.430 963 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.59 % Allowed : 15.87 % 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: 1.40 (0.29), residues: 843 helix: 2.86 (0.27), residues: 318 sheet: -0.20 (0.28), residues: 312 loop : -0.15 (0.41), residues: 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.38 seconds wall clock time: 42 minutes 55.26 seconds (2575.26 seconds total)