Starting phenix.real_space_refine on Thu Feb 15 02:01:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr4_0957/02_2024/6lr4_0957_updated.pdb" } resolution = 3.0 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= -0.000 sd= 0.004 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 2 5.49 5 S 40 5.16 5 C 7109 2.51 5 N 1709 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10838 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2444 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ESF': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.11, per 1000 atoms: 0.56 Number of scatterers: 10838 At special positions: 0 Unit cell: (112.373, 96.008, 132.011, 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 40 16.00 P 2 15.00 O 1978 8.00 N 1709 7.00 C 7109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.01 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.01 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 BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG A 821 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 49.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.635A pdb=" N LEU A 82 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.670A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.359A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 83 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.845A pdb=" N THR B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 174 removed outlier: 3.502A pdb=" N SER B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 239 removed outlier: 3.666A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.576A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 405 through 428 removed outlier: 3.695A pdb=" N ALA B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.561A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 31 through 60 removed outlier: 3.851A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 101 removed outlier: 3.978A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.624A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.680A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.838A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 239 No H-bonds generated for 'chain 'C' and resid 236 through 239' Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 38 through 41 No H-bonds generated for 'chain 'D' and resid 38 through 41' Processing helix chain 'D' and resid 50 through 80 removed outlier: 3.920A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 180 through 183 removed outlier: 6.638A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.270A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.140A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1389 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: 3.24 Time building geometry restraints manager: 4.93 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: 1721 1.32 - 1.44: 3091 1.44 - 1.56: 6236 1.56 - 1.69: 8 1.69 - 1.81: 61 Bond restraints: 11117 Sorted by residual: bond pdb=" C12 ESF B 502 " pdb=" N05 ESF B 502 " ideal model delta sigma weight residual 0.939 1.449 -0.510 2.00e-02 2.50e+03 6.51e+02 bond pdb=" C10 ESF B 502 " pdb=" C11 ESF B 502 " ideal model delta sigma weight residual 2.022 1.514 0.508 2.00e-02 2.50e+03 6.46e+02 bond pdb=" C08 ESF B 502 " pdb=" C13 ESF B 502 " ideal model delta sigma weight residual 1.138 1.498 -0.360 2.00e-02 2.50e+03 3.25e+02 bond pdb=" C09 ESF B 502 " pdb=" C11 ESF B 502 " ideal model delta sigma weight residual 1.664 1.393 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C08 ESF B 502 " pdb=" N06 ESF B 502 " ideal model delta sigma weight residual 1.666 1.451 0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 11112 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.77: 243 105.77 - 113.36: 6297 113.36 - 120.95: 5549 120.95 - 128.54: 2975 128.54 - 136.13: 101 Bond angle restraints: 15165 Sorted by residual: angle pdb=" C THR A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 120.06 126.99 -6.93 1.19e+00 7.06e-01 3.39e+01 angle pdb=" C GLY C 108 " pdb=" N ARG C 109 " pdb=" CA ARG C 109 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C PRO A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.84 113.49 6.35 1.25e+00 6.40e-01 2.58e+01 angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 129.87 -7.90 1.80e+00 3.09e-01 1.93e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 113.57 119.36 -5.79 1.38e+00 5.25e-01 1.76e+01 ... (remaining 15160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 6701 28.29 - 56.59: 158 56.59 - 84.88: 39 84.88 - 113.18: 20 113.18 - 141.47: 3 Dihedral angle restraints: 6921 sinusoidal: 3085 harmonic: 3836 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -170.81 84.81 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -147.74 -32.26 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1572 0.082 - 0.163: 216 0.163 - 0.245: 17 0.245 - 0.327: 4 0.327 - 0.409: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C2 NAG A 819 " pdb=" C1 NAG A 819 " pdb=" C3 NAG A 819 " pdb=" N2 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1809 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 ESF B 502 " -0.530 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" C12 ESF B 502 " 0.482 2.00e-02 2.50e+03 pdb=" C13 ESF B 502 " 0.037 2.00e-02 2.50e+03 pdb=" C20 ESF B 502 " -0.482 2.00e-02 2.50e+03 pdb=" N05 ESF B 502 " 0.008 2.00e-02 2.50e+03 pdb=" O01 ESF B 502 " 0.485 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 ESF B 502 " -0.093 2.00e-02 2.50e+03 7.65e-02 7.31e+01 pdb=" C19 ESF B 502 " -0.071 2.00e-02 2.50e+03 pdb=" C23 ESF B 502 " 0.026 2.00e-02 2.50e+03 pdb=" N07 ESF B 502 " 0.121 2.00e-02 2.50e+03 pdb=" O04 ESF B 502 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.027 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP C 227 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2978 2.81 - 3.33: 9647 3.33 - 3.86: 17218 3.86 - 4.38: 20243 4.38 - 4.90: 35305 Nonbonded interactions: 85391 Sorted by model distance: nonbonded pdb=" O LEU B 452 " pdb=" OG SER C 50 " model vdw 2.289 2.440 nonbonded pdb=" OG SER A 665 " pdb=" OE1 GLU A 667 " model vdw 2.290 2.440 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 280 " model vdw 2.315 2.440 nonbonded pdb=" OE2 GLU A 364 " pdb=" OG SER A 426 " model vdw 2.325 2.440 ... (remaining 85386 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 7.430 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.011 0.510 11117 Z= 0.684 Angle : 1.001 12.303 15165 Z= 0.515 Chirality : 0.059 0.409 1812 Planarity : 0.012 0.405 1831 Dihedral : 14.363 141.469 4437 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.09 % Allowed : 1.24 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: -3.96 (0.18), residues: 1304 helix: -2.19 (0.15), residues: 689 sheet: -2.06 (0.45), residues: 116 loop : -3.25 (0.22), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP C 227 HIS 0.013 0.003 HIS C 197 PHE 0.038 0.003 PHE C 132 TYR 0.027 0.003 TYR C 90 ARG 0.016 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.207 Fit side-chains REVERT: A 347 MET cc_start: 0.9101 (mtt) cc_final: 0.8826 (mtp) REVERT: A 403 LYS cc_start: 0.8566 (tttt) cc_final: 0.8262 (tppt) REVERT: A 404 SER cc_start: 0.8524 (m) cc_final: 0.8314 (m) REVERT: A 543 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8351 (mtm180) REVERT: B 165 TRP cc_start: 0.8036 (t60) cc_final: 0.7756 (t60) REVERT: B 257 ASP cc_start: 0.8325 (t70) cc_final: 0.8052 (t70) REVERT: B 430 LYS cc_start: 0.8001 (pttt) cc_final: 0.7750 (ptpt) REVERT: C 96 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7260 (mtmt) REVERT: C 117 MET cc_start: 0.8372 (mtm) cc_final: 0.8115 (mtm) REVERT: C 140 ASP cc_start: 0.7889 (m-30) cc_final: 0.7679 (m-30) REVERT: D 91 TYR cc_start: 0.8592 (m-80) cc_final: 0.8358 (m-80) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 1.1288 time to fit residues: 230.6788 Evaluate side-chains 115 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 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 163 GLN A 165 ASN A 237 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 606 GLN A 691 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11117 Z= 0.206 Angle : 0.638 9.632 15165 Z= 0.314 Chirality : 0.043 0.266 1812 Planarity : 0.005 0.045 1831 Dihedral : 12.885 144.446 2126 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.93 % Allowed : 6.83 % Favored : 90.24 % 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: -1.95 (0.22), residues: 1304 helix: -0.18 (0.19), residues: 689 sheet: -1.72 (0.47), residues: 114 loop : -2.78 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.029 0.002 PHE A 302 TYR 0.018 0.001 TYR B 256 ARG 0.010 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.086 Fit side-chains REVERT: A 63 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 283 ASP cc_start: 0.8399 (p0) cc_final: 0.8011 (p0) REVERT: A 347 MET cc_start: 0.9083 (mtt) cc_final: 0.8832 (mtp) REVERT: B 165 TRP cc_start: 0.7953 (t60) cc_final: 0.7637 (t60) REVERT: C 96 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7252 (mtmt) REVERT: C 117 MET cc_start: 0.8313 (mtm) cc_final: 0.7949 (mtm) REVERT: C 135 ILE cc_start: 0.9094 (tp) cc_final: 0.8834 (tp) outliers start: 33 outliers final: 12 residues processed: 147 average time/residue: 1.0826 time to fit residues: 172.5152 Evaluate side-chains 119 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN A 454 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN A 691 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11117 Z= 0.314 Angle : 0.667 10.212 15165 Z= 0.326 Chirality : 0.045 0.258 1812 Planarity : 0.005 0.042 1831 Dihedral : 11.355 148.106 2126 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.19 % Allowed : 9.05 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.23), residues: 1304 helix: 0.64 (0.20), residues: 685 sheet: -1.67 (0.45), residues: 124 loop : -2.62 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 36 HIS 0.005 0.001 HIS C 58 PHE 0.034 0.002 PHE A 302 TYR 0.018 0.002 TYR B 225 ARG 0.006 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.166 Fit side-chains REVERT: A 63 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: A 296 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: A 347 MET cc_start: 0.9075 (mtt) cc_final: 0.8842 (mtt) REVERT: A 601 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: B 165 TRP cc_start: 0.7948 (t60) cc_final: 0.7605 (t60) REVERT: C 96 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7193 (mtmt) REVERT: C 106 GLU cc_start: 0.4343 (OUTLIER) cc_final: 0.2946 (mp0) REVERT: C 135 ILE cc_start: 0.9068 (tp) cc_final: 0.8850 (tp) REVERT: D 81 TYR cc_start: 0.7791 (m-10) cc_final: 0.7574 (m-10) outliers start: 36 outliers final: 18 residues processed: 143 average time/residue: 1.2395 time to fit residues: 191.3325 Evaluate side-chains 129 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 163 GLN A 449 HIS A 540 GLN A 606 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11117 Z= 0.236 Angle : 0.607 10.490 15165 Z= 0.296 Chirality : 0.043 0.256 1812 Planarity : 0.004 0.041 1831 Dihedral : 10.525 148.428 2126 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.19 % Allowed : 10.83 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1304 helix: 1.09 (0.21), residues: 685 sheet: -1.59 (0.46), residues: 124 loop : -2.47 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.015 0.001 TYR B 225 ARG 0.007 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.196 Fit side-chains REVERT: A 63 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: A 296 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8068 (tp30) REVERT: A 597 LYS cc_start: 0.8357 (tttp) cc_final: 0.8034 (tptp) REVERT: B 165 TRP cc_start: 0.7887 (t60) cc_final: 0.7540 (t60) REVERT: B 257 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7583 (t70) REVERT: C 96 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7187 (mtmt) REVERT: C 106 GLU cc_start: 0.4431 (OUTLIER) cc_final: 0.3141 (mp0) REVERT: D 81 TYR cc_start: 0.7840 (m-10) cc_final: 0.7566 (m-10) outliers start: 36 outliers final: 21 residues processed: 143 average time/residue: 1.0513 time to fit residues: 164.1802 Evaluate side-chains 136 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN D 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11117 Z= 0.287 Angle : 0.633 11.097 15165 Z= 0.309 Chirality : 0.044 0.253 1812 Planarity : 0.004 0.043 1831 Dihedral : 10.318 148.427 2126 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.46 % Allowed : 11.62 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1304 helix: 1.20 (0.21), residues: 691 sheet: -1.42 (0.47), residues: 119 loop : -2.44 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.033 0.002 PHE A 302 TYR 0.017 0.002 TYR B 225 ARG 0.011 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 1.088 Fit side-chains REVERT: A 63 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: A 296 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: A 454 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 597 LYS cc_start: 0.8376 (tttp) cc_final: 0.8043 (tptp) REVERT: A 601 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: A 662 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8881 (mp) REVERT: B 165 TRP cc_start: 0.7936 (t60) cc_final: 0.7564 (t60) REVERT: C 96 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7248 (mtmt) REVERT: C 106 GLU cc_start: 0.4293 (OUTLIER) cc_final: 0.3023 (mp0) REVERT: D 81 TYR cc_start: 0.7919 (m-10) cc_final: 0.7571 (m-10) outliers start: 39 outliers final: 25 residues processed: 140 average time/residue: 1.0191 time to fit residues: 155.5724 Evaluate side-chains 139 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11117 Z= 0.237 Angle : 0.600 10.725 15165 Z= 0.293 Chirality : 0.043 0.253 1812 Planarity : 0.004 0.042 1831 Dihedral : 9.941 148.758 2126 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.19 % Allowed : 12.33 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1304 helix: 1.41 (0.21), residues: 689 sheet: -1.35 (0.47), residues: 119 loop : -2.32 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.012 0.001 TYR B 225 ARG 0.010 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.257 Fit side-chains REVERT: A 63 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 296 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: A 597 LYS cc_start: 0.8354 (tttp) cc_final: 0.8033 (tptp) REVERT: A 601 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: A 662 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8866 (mp) REVERT: B 165 TRP cc_start: 0.7891 (t60) cc_final: 0.7535 (t60) REVERT: C 96 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7324 (mtmt) REVERT: C 106 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3156 (mp0) REVERT: D 81 TYR cc_start: 0.7944 (m-10) cc_final: 0.7524 (m-10) outliers start: 36 outliers final: 20 residues processed: 139 average time/residue: 1.1396 time to fit residues: 172.3364 Evaluate side-chains 132 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11117 Z= 0.314 Angle : 0.645 11.749 15165 Z= 0.315 Chirality : 0.045 0.250 1812 Planarity : 0.004 0.043 1831 Dihedral : 9.894 148.830 2126 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.11 % Allowed : 13.13 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1304 helix: 1.38 (0.20), residues: 690 sheet: -1.30 (0.48), residues: 119 loop : -2.32 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.034 0.002 PHE A 302 TYR 0.014 0.002 TYR B 225 ARG 0.010 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.222 Fit side-chains REVERT: A 63 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: A 296 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: A 454 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: A 597 LYS cc_start: 0.8401 (tttp) cc_final: 0.8067 (tptp) REVERT: A 601 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: A 662 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 165 TRP cc_start: 0.7903 (t60) cc_final: 0.7542 (t60) REVERT: B 257 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7626 (t70) REVERT: C 96 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7308 (mtmt) REVERT: C 106 GLU cc_start: 0.4479 (OUTLIER) cc_final: 0.3179 (mp0) REVERT: D 81 TYR cc_start: 0.7972 (m-10) cc_final: 0.7549 (m-10) outliers start: 35 outliers final: 24 residues processed: 142 average time/residue: 1.0711 time to fit residues: 164.8749 Evaluate side-chains 138 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 37 optimal weight: 0.0170 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11117 Z= 0.149 Angle : 0.558 10.219 15165 Z= 0.272 Chirality : 0.041 0.256 1812 Planarity : 0.004 0.042 1831 Dihedral : 9.080 148.889 2126 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.13 % Allowed : 14.37 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1304 helix: 1.72 (0.21), residues: 692 sheet: -1.23 (0.48), residues: 119 loop : -2.16 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.025 0.001 PHE A 302 TYR 0.025 0.001 TYR B 115 ARG 0.011 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.179 Fit side-chains REVERT: A 597 LYS cc_start: 0.8323 (tttp) cc_final: 0.8025 (tptp) REVERT: A 662 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8864 (mp) REVERT: B 165 TRP cc_start: 0.7818 (t60) cc_final: 0.7480 (t60) REVERT: C 96 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7301 (mtmt) REVERT: C 106 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.3027 (mp0) REVERT: D 81 TYR cc_start: 0.7953 (m-10) cc_final: 0.7545 (m-10) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.9853 time to fit residues: 147.9554 Evaluate side-chains 133 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11117 Z= 0.271 Angle : 0.623 11.668 15165 Z= 0.302 Chirality : 0.044 0.255 1812 Planarity : 0.004 0.044 1831 Dihedral : 9.034 148.824 2126 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.31 % Allowed : 14.64 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1304 helix: 1.63 (0.20), residues: 692 sheet: -1.17 (0.48), residues: 119 loop : -2.20 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.031 0.002 PHE A 302 TYR 0.012 0.001 TYR B 225 ARG 0.010 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 2.857 Fit side-chains REVERT: A 597 LYS cc_start: 0.8370 (tttp) cc_final: 0.8046 (tptp) REVERT: A 662 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 666 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7287 (mmtt) REVERT: B 165 TRP cc_start: 0.7837 (t60) cc_final: 0.7498 (t60) REVERT: B 257 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7561 (t70) REVERT: C 96 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7322 (mtmt) REVERT: C 106 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.3399 (mp0) REVERT: D 81 TYR cc_start: 0.7949 (m-10) cc_final: 0.7540 (m-10) outliers start: 26 outliers final: 19 residues processed: 137 average time/residue: 1.1497 time to fit residues: 171.8226 Evaluate side-chains 134 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11117 Z= 0.331 Angle : 0.668 12.229 15165 Z= 0.326 Chirality : 0.045 0.256 1812 Planarity : 0.004 0.051 1831 Dihedral : 9.089 149.141 2126 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.13 % Allowed : 14.64 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1304 helix: 1.47 (0.20), residues: 693 sheet: -1.21 (0.49), residues: 119 loop : -2.24 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.034 0.002 PHE A 302 TYR 0.019 0.002 TYR B 115 ARG 0.011 0.001 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.996 Fit side-chains REVERT: A 296 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: A 597 LYS cc_start: 0.8370 (tttp) cc_final: 0.8058 (tptp) REVERT: A 662 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8905 (mp) REVERT: B 165 TRP cc_start: 0.7858 (t60) cc_final: 0.7492 (t60) REVERT: C 96 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7356 (mtmt) REVERT: C 106 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.3395 (mp0) REVERT: D 81 TYR cc_start: 0.7953 (m-10) cc_final: 0.7544 (m-10) outliers start: 24 outliers final: 19 residues processed: 126 average time/residue: 1.0898 time to fit residues: 149.4485 Evaluate side-chains 125 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.093362 restraints weight = 15631.785| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.28 r_work: 0.2933 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11117 Z= 0.256 Angle : 0.623 11.617 15165 Z= 0.304 Chirality : 0.043 0.254 1812 Planarity : 0.004 0.047 1831 Dihedral : 8.797 149.117 2126 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 15.08 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1304 helix: 1.59 (0.20), residues: 691 sheet: -1.19 (0.49), residues: 119 loop : -2.20 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.011 0.000 ARG A 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.74 seconds wall clock time: 69 minutes 53.57 seconds (4193.57 seconds total)