Starting phenix.real_space_refine on Wed Jun 26 21:36:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x54_38061/06_2024/8x54_38061_updated.pdb" } resolution = 2.9 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= 0.019 sd= 0.147 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 44 5.16 5 C 7223 2.51 5 N 1734 2.21 5 O 2005 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 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-5370/modules/chem_data/mon_lib" Total number of atoms: 11009 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 178 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5233 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: "F" 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: "G" 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: "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: "K" 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 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: 6.62, per 1000 atoms: 0.60 Number of scatterers: 11009 At special positions: 0 Unit cell: (108.692, 95.5173, 131.748, 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 44 16.00 P 3 15.00 O 2005 8.00 N 1734 7.00 C 7223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 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=2.03 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 BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 5 sheets defined 52.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'E' and resid 32 through 42 removed outlier: 3.657A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) 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 80 through 86 removed outlier: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 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 240 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' 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 431 removed outlier: 3.891A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A 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 540 through 545 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' 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 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' 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 79 through 102 removed outlier: 3.752A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 Processing helix chain 'B' and resid 159 through 174 removed outlier: 3.596A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.847A 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 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.920A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 428 removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 removed outlier: 3.794A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 29 through 60 removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 102 removed outlier: 3.738A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.535A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.587A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (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 240 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.790A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 48 through 80 removed outlier: 3.839A pdb=" N SER D 51 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TRP D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 60 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 61 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 72 " --> pdb=" O ILE D 69 " (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 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (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: 7.447A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.152A 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: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 504 hydrogen bonds defined for protein. 1431 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: 2.97 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 86 1.23 - 1.37: 3611 1.37 - 1.52: 5087 1.52 - 1.67: 2433 1.67 - 1.81: 67 Bond restraints: 11284 Sorted by residual: bond pdb=" C LEU B 241 " pdb=" N PRO B 242 " ideal model delta sigma weight residual 1.331 1.512 -0.181 1.21e-02 6.83e+03 2.24e+02 bond pdb=" C GLY B 384 " pdb=" O GLY B 384 " ideal model delta sigma weight residual 1.236 1.090 0.146 1.08e-02 8.57e+03 1.82e+02 bond pdb=" C ALA B 434 " pdb=" O ALA B 434 " ideal model delta sigma weight residual 1.236 1.388 -0.152 1.19e-02 7.06e+03 1.64e+02 bond pdb=" C ILE B 437 " pdb=" O ILE B 437 " ideal model delta sigma weight residual 1.240 1.095 0.144 1.18e-02 7.18e+03 1.49e+02 bond pdb=" C SER B 438 " pdb=" O SER B 438 " ideal model delta sigma weight residual 1.236 1.081 0.155 1.29e-02 6.01e+03 1.44e+02 ... (remaining 11279 not shown) Histogram of bond angle deviations from ideal: 96.68 - 106.16: 288 106.16 - 115.64: 7242 115.64 - 125.13: 7601 125.13 - 134.61: 246 134.61 - 144.10: 3 Bond angle restraints: 15380 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.10 -28.67 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C THR B 116 " pdb=" N PRO B 117 " pdb=" CA PRO B 117 " ideal model delta sigma weight residual 119.84 137.84 -18.00 1.25e+00 6.40e-01 2.07e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.58 -12.34 1.04e+00 9.25e-01 1.41e+02 angle pdb=" CA THR B 116 " pdb=" C THR B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 117.57 127.64 -10.07 8.70e-01 1.32e+00 1.34e+02 angle pdb=" C ALA B 79 " pdb=" N LYS B 80 " pdb=" CA LYS B 80 " ideal model delta sigma weight residual 120.44 133.39 -12.95 1.30e+00 5.92e-01 9.93e+01 ... (remaining 15375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6726 23.50 - 47.00: 228 47.00 - 70.49: 53 70.49 - 93.99: 21 93.99 - 117.49: 18 Dihedral angle restraints: 7046 sinusoidal: 3149 harmonic: 3897 Sorted by residual: 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 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -104.14 -18.46 0 2.50e+00 1.60e-01 5.45e+01 dihedral pdb=" C GLN B 112 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " pdb=" CB GLN B 112 " ideal model delta harmonic sigma weight residual -122.60 -106.11 -16.49 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 7043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1778 0.134 - 0.268: 49 0.268 - 0.402: 14 0.402 - 0.536: 2 0.536 - 0.670: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CB VAL E 46 " pdb=" CA VAL E 46 " pdb=" CG1 VAL E 46 " pdb=" CG2 VAL E 46 " both_signs ideal model delta sigma weight residual False -2.63 -1.96 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA VAL E 46 " pdb=" N VAL E 46 " pdb=" C VAL E 46 " pdb=" CB VAL E 46 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 1841 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.117 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.188 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 439 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ILE B 439 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE B 439 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 440 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 112 " -0.019 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C GLN B 112 " 0.069 2.00e-02 2.50e+03 pdb=" O GLN B 112 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU B 113 " -0.023 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 2 2.26 - 2.92: 4422 2.92 - 3.58: 15452 3.58 - 4.24: 25612 4.24 - 4.90: 43076 Nonbonded interactions: 88564 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.597 2.776 nonbonded pdb=" O VAL E 39 " pdb=" OG1 THR E 43 " model vdw 2.204 2.440 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.264 2.440 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.311 2.440 ... (remaining 88559 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 0.320 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: 1.710 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.790 Find NCS groups from input model: 0.310 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 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 : 0.010 0.184 11284 Z= 0.636 Angle : 1.149 28.667 15380 Z= 0.682 Chirality : 0.068 0.670 1844 Planarity : 0.007 0.071 1850 Dihedral : 14.622 117.489 4519 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.05 % Allowed : 2.79 % Favored : 96.16 % Cbeta Deviations : 0.48 % 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: -3.47 (0.18), residues: 1325 helix: -1.89 (0.15), residues: 728 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 46 LYS cc_start: 0.6443 (mmmm) cc_final: 0.5864 (mmtm) REVERT: A 58 HIS cc_start: 0.6605 (m90) cc_final: 0.6042 (m90) REVERT: A 77 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7376 (mm-30) REVERT: A 78 LYS cc_start: 0.6246 (ptpt) cc_final: 0.5801 (pttm) REVERT: A 81 ASP cc_start: 0.6419 (m-30) cc_final: 0.6081 (m-30) REVERT: A 94 TYR cc_start: 0.7197 (m-80) cc_final: 0.6732 (m-80) REVERT: A 155 GLU cc_start: 0.7276 (mp0) cc_final: 0.7004 (mp0) REVERT: A 221 MET cc_start: 0.7019 (mmp) cc_final: 0.6772 (mmp) REVERT: A 284 SER cc_start: 0.8339 (p) cc_final: 0.8062 (m) REVERT: A 344 VAL cc_start: 0.5933 (t) cc_final: 0.5636 (t) REVERT: A 351 LYS cc_start: 0.7031 (mmtp) cc_final: 0.6802 (mtpt) REVERT: A 528 LYS cc_start: 0.6068 (tttt) cc_final: 0.5812 (tttm) REVERT: A 531 ASN cc_start: 0.6002 (m-40) cc_final: 0.5799 (m-40) REVERT: A 606 GLN cc_start: 0.5167 (mt0) cc_final: 0.4879 (mt0) REVERT: A 693 LYS cc_start: 0.6922 (mmtp) cc_final: 0.6660 (mmmm) REVERT: B 430 LYS cc_start: 0.6481 (mtpt) cc_final: 0.5541 (pttt) REVERT: B 436 PRO cc_start: 0.7053 (OUTLIER) cc_final: 0.6835 (Cg_exo) REVERT: C 28 ASP cc_start: 0.6885 (m-30) cc_final: 0.6666 (t0) REVERT: C 29 PRO cc_start: 0.7362 (Cg_endo) cc_final: 0.7125 (Cg_exo) REVERT: C 113 SER cc_start: 0.6085 (m) cc_final: 0.5774 (p) REVERT: C 183 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6827 (tp30) outliers start: 12 outliers final: 2 residues processed: 247 average time/residue: 0.9235 time to fit residues: 250.5876 Evaluate side-chains 139 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 436 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.0010 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 420 GLN A 449 HIS A 454 GLN A 535 GLN A 606 GLN A 691 ASN B 385 ASN B 463 HIS D 33 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11284 Z= 0.154 Angle : 0.612 11.863 15380 Z= 0.295 Chirality : 0.043 0.290 1844 Planarity : 0.004 0.039 1850 Dihedral : 12.831 102.918 2180 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.14 % Allowed : 10.82 % Favored : 86.04 % 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: -1.35 (0.22), residues: 1325 helix: 0.10 (0.19), residues: 714 sheet: -0.95 (0.48), residues: 112 loop : -2.34 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 227 HIS 0.008 0.001 HIS C 197 PHE 0.026 0.002 PHE A 302 TYR 0.014 0.001 TYR A 565 ARG 0.003 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.254 Fit side-chains REVERT: E 51 MET cc_start: 0.8600 (ttm) cc_final: 0.8149 (ttp) REVERT: A 37 GLU cc_start: 0.6430 (pt0) cc_final: 0.5887 (mt-10) REVERT: A 46 LYS cc_start: 0.6367 (mmmm) cc_final: 0.5868 (mmtm) REVERT: A 58 HIS cc_start: 0.6737 (m90) cc_final: 0.6283 (m90) REVERT: A 77 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7528 (mm-30) REVERT: A 78 LYS cc_start: 0.6460 (ptpt) cc_final: 0.5866 (pttm) REVERT: A 94 TYR cc_start: 0.7092 (m-80) cc_final: 0.6495 (m-80) REVERT: A 155 GLU cc_start: 0.7238 (mp0) cc_final: 0.6980 (mp0) REVERT: A 235 SER cc_start: 0.5934 (t) cc_final: 0.5707 (p) REVERT: A 259 MET cc_start: 0.8484 (tpt) cc_final: 0.8109 (tpp) REVERT: A 351 LYS cc_start: 0.7103 (mmtp) cc_final: 0.6873 (mtpt) REVERT: A 364 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.4928 (tt0) REVERT: A 374 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6239 (mt) REVERT: A 395 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6688 (mm-30) REVERT: A 403 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6450 (tttm) REVERT: A 689 CYS cc_start: 0.6700 (t) cc_final: 0.6384 (m) REVERT: B 84 MET cc_start: 0.6400 (mtp) cc_final: 0.6181 (mtt) REVERT: B 283 PHE cc_start: 0.5955 (m-80) cc_final: 0.5598 (m-80) REVERT: B 430 LYS cc_start: 0.6311 (mtpt) cc_final: 0.5371 (pttt) REVERT: C 113 SER cc_start: 0.6037 (m) cc_final: 0.5799 (p) outliers start: 36 outliers final: 10 residues processed: 170 average time/residue: 0.9489 time to fit residues: 177.8275 Evaluate side-chains 133 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11284 Z= 0.155 Angle : 0.570 12.206 15380 Z= 0.274 Chirality : 0.042 0.254 1844 Planarity : 0.004 0.040 1850 Dihedral : 10.852 108.836 2174 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.32 % Allowed : 12.30 % Favored : 84.38 % 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: -0.65 (0.23), residues: 1325 helix: 0.80 (0.19), residues: 714 sheet: -1.18 (0.42), residues: 138 loop : -2.11 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.014 0.001 TYR A 565 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6392 (pt0) cc_final: 0.5851 (mt-10) REVERT: A 46 LYS cc_start: 0.6428 (mmmm) cc_final: 0.5865 (mmtm) REVERT: A 77 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7485 (mm-30) REVERT: A 155 GLU cc_start: 0.7127 (mp0) cc_final: 0.6839 (mp0) REVERT: A 184 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: A 351 LYS cc_start: 0.7128 (mmtp) cc_final: 0.6909 (mtpt) REVERT: A 395 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6617 (mm-30) REVERT: A 624 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7592 (m) REVERT: A 632 SER cc_start: 0.7555 (m) cc_final: 0.7325 (t) REVERT: A 689 CYS cc_start: 0.6169 (t) cc_final: 0.5869 (m) REVERT: B 210 MET cc_start: 0.6245 (mmp) cc_final: 0.5948 (mmm) REVERT: B 283 PHE cc_start: 0.5947 (m-80) cc_final: 0.5688 (m-80) outliers start: 38 outliers final: 13 residues processed: 163 average time/residue: 0.8536 time to fit residues: 154.8938 Evaluate side-chains 138 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 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 385 GLN A 420 GLN B 385 ASN C 171 HIS D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11284 Z= 0.149 Angle : 0.551 11.558 15380 Z= 0.263 Chirality : 0.041 0.239 1844 Planarity : 0.003 0.041 1850 Dihedral : 9.949 103.541 2172 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.23 % Allowed : 14.14 % Favored : 82.64 % 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: -0.16 (0.23), residues: 1325 helix: 1.22 (0.20), residues: 716 sheet: -1.21 (0.43), residues: 138 loop : -1.86 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.027 0.001 PHE A 302 TYR 0.012 0.001 TYR A 565 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6335 (pt0) cc_final: 0.5821 (mt-10) REVERT: A 46 LYS cc_start: 0.6405 (mmmm) cc_final: 0.5946 (mmtm) REVERT: A 77 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7440 (mm-30) REVERT: A 155 GLU cc_start: 0.7068 (mp0) cc_final: 0.6731 (mp0) REVERT: A 184 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6437 (mt-10) REVERT: A 259 MET cc_start: 0.8613 (tpt) cc_final: 0.8214 (tpp) REVERT: A 351 LYS cc_start: 0.7290 (mmtp) cc_final: 0.7084 (mtpt) REVERT: A 385 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.6140 (mt0) REVERT: A 395 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6634 (mm-30) REVERT: A 396 ASP cc_start: 0.6483 (m-30) cc_final: 0.6178 (m-30) REVERT: A 403 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6471 (tttm) REVERT: A 624 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 689 CYS cc_start: 0.6168 (t) cc_final: 0.5857 (m) REVERT: B 210 MET cc_start: 0.6057 (mmp) cc_final: 0.5746 (mmm) outliers start: 37 outliers final: 15 residues processed: 149 average time/residue: 0.9813 time to fit residues: 160.7503 Evaluate side-chains 133 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 31 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 220 HIS D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11284 Z= 0.210 Angle : 0.580 12.671 15380 Z= 0.278 Chirality : 0.045 0.634 1844 Planarity : 0.004 0.041 1850 Dihedral : 9.694 88.647 2172 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.84 % Allowed : 14.14 % Favored : 82.02 % 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: -0.09 (0.23), residues: 1325 helix: 1.23 (0.20), residues: 725 sheet: -1.09 (0.42), residues: 140 loop : -1.83 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.008 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.015 0.001 TYR C 218 ARG 0.006 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6323 (pt0) cc_final: 0.5805 (mt-10) REVERT: A 46 LYS cc_start: 0.6414 (mmmm) cc_final: 0.5924 (mmtm) REVERT: A 77 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7398 (mm-30) REVERT: A 150 ASN cc_start: 0.7867 (p0) cc_final: 0.7309 (m-40) REVERT: A 155 GLU cc_start: 0.6997 (mp0) cc_final: 0.6701 (mp0) REVERT: A 184 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: A 351 LYS cc_start: 0.7334 (mmtp) cc_final: 0.7124 (mtpt) REVERT: A 364 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5028 (tt0) REVERT: A 385 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: A 395 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6705 (tp30) REVERT: A 396 ASP cc_start: 0.6491 (m-30) cc_final: 0.6163 (m-30) REVERT: A 403 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6554 (tttm) REVERT: A 541 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6602 (t0) REVERT: A 624 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 689 CYS cc_start: 0.6072 (t) cc_final: 0.5813 (m) outliers start: 44 outliers final: 21 residues processed: 140 average time/residue: 0.9826 time to fit residues: 151.2741 Evaluate side-chains 132 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11284 Z= 0.267 Angle : 0.627 12.853 15380 Z= 0.301 Chirality : 0.046 0.700 1844 Planarity : 0.004 0.081 1850 Dihedral : 9.368 75.476 2172 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.80 % Allowed : 13.70 % Favored : 81.50 % 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: -0.12 (0.23), residues: 1325 helix: 1.18 (0.20), residues: 728 sheet: -1.08 (0.43), residues: 140 loop : -1.81 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 74 HIS 0.009 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.017 0.002 TYR C 218 ARG 0.005 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 114 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 46 LYS cc_start: 0.6321 (mmmm) cc_final: 0.5978 (mmtm) REVERT: A 77 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7325 (mm-30) REVERT: A 150 ASN cc_start: 0.7870 (p0) cc_final: 0.7391 (m-40) REVERT: A 155 GLU cc_start: 0.6989 (mp0) cc_final: 0.6666 (mp0) REVERT: A 184 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6418 (mt-10) REVERT: A 351 LYS cc_start: 0.7333 (mmtp) cc_final: 0.7109 (mttt) REVERT: A 364 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.5334 (tt0) REVERT: A 374 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5719 (mt) REVERT: A 396 ASP cc_start: 0.6631 (m-30) cc_final: 0.6255 (m-30) REVERT: A 403 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6700 (tttm) REVERT: A 541 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6517 (t0) REVERT: A 544 SER cc_start: 0.6977 (m) cc_final: 0.6732 (p) REVERT: A 619 ARG cc_start: 0.4210 (OUTLIER) cc_final: 0.3881 (ptt180) REVERT: A 624 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7807 (m) REVERT: A 655 ASP cc_start: 0.5848 (t0) cc_final: 0.5256 (t70) REVERT: A 689 CYS cc_start: 0.6134 (t) cc_final: 0.5845 (m) REVERT: D 91 TYR cc_start: 0.7525 (m-80) cc_final: 0.7079 (m-80) outliers start: 55 outliers final: 23 residues processed: 155 average time/residue: 0.9514 time to fit residues: 162.4397 Evaluate side-chains 139 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 72 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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: 0.5737 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11284 Z= 0.248 Angle : 0.606 12.927 15380 Z= 0.290 Chirality : 0.045 0.647 1844 Planarity : 0.004 0.072 1850 Dihedral : 9.173 74.947 2172 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.01 % Allowed : 15.53 % Favored : 80.45 % 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: -0.01 (0.23), residues: 1325 helix: 1.25 (0.20), residues: 728 sheet: -0.87 (0.44), residues: 134 loop : -1.79 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.008 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.014 0.001 TYR C 218 ARG 0.003 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.7480 (mp) cc_final: 0.7231 (tt) REVERT: E 49 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8054 (mt) REVERT: A 46 LYS cc_start: 0.6300 (mmmm) cc_final: 0.5833 (mmtm) REVERT: A 77 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7217 (mm-30) REVERT: A 150 ASN cc_start: 0.7854 (p0) cc_final: 0.7450 (m-40) REVERT: A 155 GLU cc_start: 0.6964 (mp0) cc_final: 0.6652 (mp0) REVERT: A 351 LYS cc_start: 0.7439 (mmtp) cc_final: 0.6792 (mppt) REVERT: A 364 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.5523 (tt0) REVERT: A 365 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6989 (mp) REVERT: A 396 ASP cc_start: 0.6639 (m-30) cc_final: 0.6338 (m-30) REVERT: A 403 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6919 (ttpp) REVERT: A 541 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6909 (t0) REVERT: A 544 SER cc_start: 0.6957 (m) cc_final: 0.6721 (p) REVERT: A 582 THR cc_start: 0.5724 (m) cc_final: 0.5442 (p) REVERT: A 619 ARG cc_start: 0.4437 (OUTLIER) cc_final: 0.4074 (ptt180) REVERT: A 624 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7851 (m) REVERT: A 689 CYS cc_start: 0.6149 (t) cc_final: 0.5859 (m) REVERT: B 430 LYS cc_start: 0.6321 (mtpt) cc_final: 0.5908 (mtmm) REVERT: D 91 TYR cc_start: 0.7496 (m-80) cc_final: 0.7141 (m-80) outliers start: 46 outliers final: 25 residues processed: 147 average time/residue: 1.0677 time to fit residues: 171.8996 Evaluate side-chains 134 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.5705 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11284 Z= 0.134 Angle : 0.543 12.585 15380 Z= 0.257 Chirality : 0.043 0.626 1844 Planarity : 0.003 0.054 1850 Dihedral : 8.644 74.491 2172 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 2.18 % Allowed : 17.71 % Favored : 80.10 % 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: 0.34 (0.24), residues: 1325 helix: 1.58 (0.20), residues: 723 sheet: -0.87 (0.44), residues: 138 loop : -1.63 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 604 HIS 0.005 0.001 HIS C 197 PHE 0.025 0.001 PHE A 302 TYR 0.011 0.001 TYR A 569 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6272 (pt0) cc_final: 0.5758 (mt-10) REVERT: A 46 LYS cc_start: 0.6289 (mmmm) cc_final: 0.5837 (mmtm) REVERT: A 77 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7205 (mm-30) REVERT: A 150 ASN cc_start: 0.7924 (p0) cc_final: 0.7608 (m-40) REVERT: A 155 GLU cc_start: 0.6923 (mp0) cc_final: 0.6551 (mp0) REVERT: A 351 LYS cc_start: 0.7250 (mmtp) cc_final: 0.6592 (mppt) REVERT: A 396 ASP cc_start: 0.6621 (m-30) cc_final: 0.6388 (m-30) REVERT: A 403 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6919 (ttpp) REVERT: A 541 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7035 (t0) REVERT: A 582 THR cc_start: 0.5722 (OUTLIER) cc_final: 0.5434 (p) REVERT: A 624 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7786 (m) REVERT: A 689 CYS cc_start: 0.6100 (t) cc_final: 0.5823 (m) REVERT: B 283 PHE cc_start: 0.5182 (m-80) cc_final: 0.4978 (m-80) REVERT: C 117 MET cc_start: 0.6396 (mtp) cc_final: 0.6072 (mtt) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 1.0112 time to fit residues: 141.1156 Evaluate side-chains 119 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 137 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.5720 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11284 Z= 0.178 Angle : 0.569 12.822 15380 Z= 0.269 Chirality : 0.044 0.631 1844 Planarity : 0.004 0.055 1850 Dihedral : 8.368 73.927 2172 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 2.27 % Allowed : 17.89 % Favored : 79.84 % 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: 0.38 (0.24), residues: 1325 helix: 1.59 (0.20), residues: 723 sheet: -0.73 (0.45), residues: 130 loop : -1.61 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.028 0.001 PHE A 302 TYR 0.012 0.001 TYR A 337 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.7596 (mp) cc_final: 0.7303 (tt) REVERT: A 46 LYS cc_start: 0.6295 (mmmm) cc_final: 0.5876 (mmtm) REVERT: A 77 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7264 (mm-30) REVERT: A 150 ASN cc_start: 0.7920 (p0) cc_final: 0.7656 (m-40) REVERT: A 155 GLU cc_start: 0.6933 (mp0) cc_final: 0.6624 (mp0) REVERT: A 184 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: A 266 THR cc_start: 0.7795 (m) cc_final: 0.7564 (p) REVERT: A 351 LYS cc_start: 0.7214 (mmtp) cc_final: 0.6568 (mppt) REVERT: A 396 ASP cc_start: 0.6567 (m-30) cc_final: 0.6334 (m-30) REVERT: A 403 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6926 (ttpp) REVERT: A 582 THR cc_start: 0.5547 (OUTLIER) cc_final: 0.5274 (p) REVERT: A 619 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.4138 (ptt180) REVERT: A 624 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (m) REVERT: A 655 ASP cc_start: 0.5818 (t0) cc_final: 0.5089 (t70) REVERT: A 689 CYS cc_start: 0.6206 (t) cc_final: 0.5941 (m) REVERT: B 233 MET cc_start: 0.5950 (tpt) cc_final: 0.5721 (tpt) outliers start: 26 outliers final: 16 residues processed: 125 average time/residue: 1.0664 time to fit residues: 145.9492 Evaluate side-chains 125 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 0.0030 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11284 Z= 0.125 Angle : 0.530 12.790 15380 Z= 0.249 Chirality : 0.042 0.624 1844 Planarity : 0.004 0.075 1850 Dihedral : 7.944 73.804 2172 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.75 % Allowed : 18.50 % Favored : 79.76 % 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: 0.56 (0.24), residues: 1325 helix: 1.80 (0.20), residues: 720 sheet: -0.74 (0.44), residues: 138 loop : -1.60 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 604 HIS 0.004 0.001 HIS A 553 PHE 0.024 0.001 PHE A 302 TYR 0.010 0.001 TYR A 569 ARG 0.002 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.7495 (mp) cc_final: 0.7220 (tt) REVERT: A 46 LYS cc_start: 0.6327 (mmmm) cc_final: 0.5910 (mmtm) REVERT: A 77 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7259 (mm-30) REVERT: A 150 ASN cc_start: 0.7884 (p0) cc_final: 0.7662 (m-40) REVERT: A 155 GLU cc_start: 0.6879 (mp0) cc_final: 0.6492 (mp0) REVERT: A 266 THR cc_start: 0.7802 (m) cc_final: 0.7563 (p) REVERT: A 351 LYS cc_start: 0.7237 (mmtp) cc_final: 0.6578 (mppt) REVERT: A 396 ASP cc_start: 0.6509 (m-30) cc_final: 0.6262 (m-30) REVERT: A 403 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.7085 (ttmt) REVERT: A 582 THR cc_start: 0.5527 (OUTLIER) cc_final: 0.5257 (p) REVERT: A 624 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7788 (m) REVERT: A 689 CYS cc_start: 0.6075 (t) cc_final: 0.5814 (m) REVERT: B 145 VAL cc_start: 0.5537 (p) cc_final: 0.5281 (m) REVERT: C 117 MET cc_start: 0.6396 (mtp) cc_final: 0.6070 (mtt) outliers start: 20 outliers final: 10 residues processed: 122 average time/residue: 1.0927 time to fit residues: 145.6560 Evaluate side-chains 121 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122101 restraints weight = 12999.463| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.22 r_work: 0.3343 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11284 Z= 0.253 Angle : 0.615 12.863 15380 Z= 0.292 Chirality : 0.045 0.621 1844 Planarity : 0.004 0.078 1850 Dihedral : 8.141 73.398 2172 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.36 % Allowed : 17.89 % Favored : 79.76 % 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: 0.30 (0.24), residues: 1325 helix: 1.51 (0.20), residues: 728 sheet: -0.63 (0.46), residues: 130 loop : -1.69 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.008 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.016 0.002 TYR C 218 ARG 0.003 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.03 seconds wall clock time: 63 minutes 19.83 seconds (3799.83 seconds total)