Starting phenix.real_space_refine on Thu Feb 15 01:26:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/02_2024/8k8e_36948_updated.pdb" } resolution = 2.6 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= 0.002 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 1 5.49 5 S 40 5.16 5 C 7044 2.51 5 N 1705 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 475": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10716 Number of models: 1 Model: "" Number of chains: 10 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: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2394 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain breaks: 2 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: "G" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 133 Unusual residues: {'BOC': 1, 'JUU': 1} Classifications: {'peptide': 16, 'undetermined': 2} Link IDs: {'LINK_CNp': 1, 'TRANS': 14, None: 2} Not linked: pdbres="VAL G 15 " pdbres="JUU G 16 " Not linked: pdbres="JUU G 16 " pdbres="LEU G 17 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'JUU:plan-3': 1, 'AIB:plan-1': 3} Unresolved non-hydrogen planarities: 4 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.29, per 1000 atoms: 0.59 Number of scatterers: 10716 At special positions: 0 Unit cell: (112.58, 94.1775, 130.982, 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 1 15.00 O 1926 8.00 N 1705 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 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 Atom "HETATM10322 O2 BOC G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-3 " BMA F 1 " - " BMA F 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " BMA F 1 " - " BMA F 3 " NAG-ASN " NAG A 801 " - " ASN A 45 " " NAG A 802 " - " ASN A 435 " " NAG A 803 " - " ASN A 573 " " NAG A 804 " - " ASN A 530 " " NAG A 805 " - " ASN A 506 " " NAG A 806 " - " ASN A 187 " " NAG E 1 " - " ASN A 55 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 3 sheets defined 54.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 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: 3.503A pdb=" N TRP A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' 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 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.981A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.590A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 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 407 removed outlier: 3.813A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 460 through 463 No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.703A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.254A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 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 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) 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 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 125 through 154 Processing helix chain 'B' and resid 161 through 188 removed outlier: 3.885A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) 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: 3.512A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.599A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 3 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 29 through 60 removed outlier: 3.761A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.513A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 142 removed outlier: 6.002A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.632A pdb=" N GLU C 183 " --> pdb=" O PHE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 206 removed outlier: 3.745A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.520A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.992A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 42 removed outlier: 5.282A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 84 removed outlier: 3.685A pdb=" N ILE D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'G' and resid 3 through 7 removed outlier: 4.126A pdb=" N ILE G 7 " --> pdb=" O AIB G 4 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.634A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.356A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.121A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1563 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: 3.27 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.44: 3135 1.44 - 1.57: 6163 1.57 - 1.70: 3 1.70 - 1.84: 61 Bond restraints: 10994 Sorted by residual: bond pdb=" C BOC G 1 " pdb=" O1 BOC G 1 " ideal model delta sigma weight residual 1.410 1.195 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C VLM G 18 " pdb=" NT VLM G 18 " ideal model delta sigma weight residual 1.338 1.451 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C BOC G 1 " pdb=" O2 BOC G 1 " ideal model delta sigma weight residual 1.250 1.336 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta sigma weight residual 1.458 1.488 -0.031 7.40e-03 1.83e+04 1.71e+01 bond pdb=" CT BOC G 1 " pdb=" O2 BOC G 1 " ideal model delta sigma weight residual 1.410 1.484 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 10989 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.55: 319 106.55 - 113.42: 6130 113.42 - 120.29: 4005 120.29 - 127.16: 4415 127.16 - 134.04: 132 Bond angle restraints: 15001 Sorted by residual: angle pdb=" CA ASN A 562 " pdb=" CB ASN A 562 " pdb=" CG ASN A 562 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASN A 562 " pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 120.90 117.07 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 114.75 110.35 4.40 1.26e+00 6.30e-01 1.22e+01 angle pdb=" CA GLU D 40 " pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA GLU C 106 " pdb=" CB GLU C 106 " pdb=" CG GLU C 106 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 6199 22.74 - 45.48: 393 45.48 - 68.22: 58 68.22 - 90.95: 32 90.95 - 113.69: 12 Dihedral angle restraints: 6694 sinusoidal: 2845 harmonic: 3849 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 -170.34 84.34 1 1.00e+01 1.00e-02 8.65e+01 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 -162.32 76.32 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 213 " pdb=" CB CYS A 213 " ideal model delta sinusoidal sigma weight residual 93.00 40.91 52.09 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 6691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1685 0.093 - 0.185: 71 0.185 - 0.278: 7 0.278 - 0.371: 1 0.371 - 0.463: 2 Chirality restraints: 1766 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.95e+00 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1763 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 211 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 40 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" CD GLU D 40 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU D 40 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 40 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 264 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASN A 264 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 264 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 265 " 0.010 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1645 2.75 - 3.29: 10584 3.29 - 3.83: 18119 3.83 - 4.36: 21110 4.36 - 4.90: 36454 Nonbonded interactions: 87912 Sorted by model distance: nonbonded pdb=" OG SER C 113 " pdb=" OE1 GLN C 116 " model vdw 2.218 2.440 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.222 2.520 nonbonded pdb=" N GLU D 9 " pdb=" OE1 GLU D 9 " model vdw 2.243 2.520 nonbonded pdb=" O SER A 235 " pdb=" OG SER A 238 " model vdw 2.245 2.440 nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.257 2.440 ... (remaining 87907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.260 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: 7.230 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 33.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 54.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.005 0.215 10994 Z= 0.315 Angle : 0.681 8.053 15001 Z= 0.347 Chirality : 0.047 0.463 1766 Planarity : 0.004 0.051 1824 Dihedral : 16.306 113.692 4201 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.33 % Allowed : 15.68 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1299 helix: 1.79 (0.20), residues: 682 sheet: -0.72 (0.49), residues: 108 loop : -1.61 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.024 0.001 PHE A 302 TYR 0.020 0.001 TYR D 47 ARG 0.014 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8876 (tpp) cc_final: 0.8495 (mmt) REVERT: A 237 GLN cc_start: 0.9025 (tp40) cc_final: 0.8155 (tm-30) REVERT: B 112 GLN cc_start: 0.8641 (mt0) cc_final: 0.8433 (pt0) REVERT: B 159 TYR cc_start: 0.4058 (t80) cc_final: 0.3738 (t80) REVERT: C 96 LYS cc_start: 0.7423 (mttt) cc_final: 0.7003 (tppt) REVERT: C 115 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7160 (ttt180) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 1.2719 time to fit residues: 152.5777 Evaluate side-chains 90 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10994 Z= 0.252 Angle : 0.581 7.998 15001 Z= 0.297 Chirality : 0.043 0.401 1766 Planarity : 0.004 0.052 1824 Dihedral : 11.238 98.935 1905 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.72 % Allowed : 13.91 % Favored : 82.37 % 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: 0.68 (0.24), residues: 1299 helix: 2.05 (0.20), residues: 685 sheet: -0.88 (0.49), residues: 112 loop : -1.58 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 PHE 0.025 0.001 PHE A 302 TYR 0.014 0.001 TYR B 466 ARG 0.005 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 91 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9064 (tpp) cc_final: 0.8857 (mmt) REVERT: A 121 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8919 (tp) REVERT: A 237 GLN cc_start: 0.9017 (tp40) cc_final: 0.7893 (tm-30) REVERT: A 626 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8815 (mtt-85) REVERT: B 112 GLN cc_start: 0.8563 (mt0) cc_final: 0.8317 (pt0) REVERT: B 159 TYR cc_start: 0.4001 (t80) cc_final: 0.3640 (t80) REVERT: C 96 LYS cc_start: 0.7390 (mttt) cc_final: 0.6949 (tppt) outliers start: 42 outliers final: 17 residues processed: 122 average time/residue: 0.9912 time to fit residues: 133.7572 Evaluate side-chains 99 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10994 Z= 0.176 Angle : 0.539 7.269 15001 Z= 0.274 Chirality : 0.041 0.383 1766 Planarity : 0.004 0.054 1824 Dihedral : 9.713 91.168 1898 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.63 % Allowed : 15.50 % Favored : 80.87 % 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: 0.85 (0.24), residues: 1299 helix: 2.22 (0.20), residues: 684 sheet: -0.87 (0.45), residues: 129 loop : -1.53 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.011 0.001 TYR B 466 ARG 0.008 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8904 (tp40) cc_final: 0.7902 (tm-30) REVERT: B 159 TYR cc_start: 0.3987 (t80) cc_final: 0.3664 (t80) REVERT: C 96 LYS cc_start: 0.7350 (mttt) cc_final: 0.6953 (tppt) outliers start: 41 outliers final: 20 residues processed: 121 average time/residue: 0.8579 time to fit residues: 116.2645 Evaluate side-chains 101 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain G residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 243 ASN A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10994 Z= 0.407 Angle : 0.640 9.024 15001 Z= 0.324 Chirality : 0.046 0.422 1766 Planarity : 0.004 0.053 1824 Dihedral : 9.432 86.527 1894 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.61 % Allowed : 15.68 % Favored : 79.72 % 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: 0.77 (0.24), residues: 1299 helix: 2.17 (0.20), residues: 684 sheet: -0.99 (0.46), residues: 125 loop : -1.57 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.009 0.001 HIS A 449 PHE 0.026 0.002 PHE A 302 TYR 0.022 0.002 TYR B 466 ARG 0.006 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 84 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8864 (tp40) cc_final: 0.7910 (tm-30) REVERT: A 414 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8589 (mtm110) REVERT: B 159 TYR cc_start: 0.4137 (t80) cc_final: 0.3818 (t80) REVERT: B 278 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.3688 (mpt180) REVERT: C 96 LYS cc_start: 0.7103 (mttt) cc_final: 0.6703 (tppt) REVERT: D 11 LYS cc_start: 0.8477 (mttp) cc_final: 0.8192 (mttt) outliers start: 52 outliers final: 22 residues processed: 125 average time/residue: 0.9907 time to fit residues: 136.3820 Evaluate side-chains 104 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain G residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10994 Z= 0.275 Angle : 0.589 7.989 15001 Z= 0.301 Chirality : 0.044 0.413 1766 Planarity : 0.004 0.049 1824 Dihedral : 8.850 80.876 1894 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.07 % Allowed : 16.30 % Favored : 79.63 % 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: 0.83 (0.24), residues: 1299 helix: 2.22 (0.20), residues: 684 sheet: -1.02 (0.46), residues: 125 loop : -1.52 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 PHE 0.025 0.001 PHE A 302 TYR 0.018 0.001 TYR B 466 ARG 0.009 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 85 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8858 (tp40) cc_final: 0.7834 (tm-30) REVERT: B 159 TYR cc_start: 0.4053 (t80) cc_final: 0.3710 (t80) REVERT: B 278 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.3493 (mpt180) REVERT: C 96 LYS cc_start: 0.7111 (mttt) cc_final: 0.6713 (tppt) REVERT: D 11 LYS cc_start: 0.8419 (mttp) cc_final: 0.8142 (mttt) outliers start: 46 outliers final: 22 residues processed: 122 average time/residue: 0.9278 time to fit residues: 125.8504 Evaluate side-chains 101 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain G residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.0060 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10994 Z= 0.236 Angle : 0.569 7.735 15001 Z= 0.291 Chirality : 0.043 0.384 1766 Planarity : 0.004 0.052 1824 Dihedral : 8.179 83.020 1894 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.90 % Allowed : 16.65 % Favored : 79.45 % 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: 0.90 (0.24), residues: 1299 helix: 2.28 (0.20), residues: 685 sheet: -1.01 (0.46), residues: 125 loop : -1.48 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.025 0.001 PHE A 302 TYR 0.014 0.001 TYR B 466 ARG 0.010 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8847 (tp40) cc_final: 0.7862 (tm-30) REVERT: A 414 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8914 (mtp180) REVERT: B 159 TYR cc_start: 0.3950 (t80) cc_final: 0.3621 (t80) REVERT: B 278 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.3378 (mpt180) REVERT: C 96 LYS cc_start: 0.7094 (mttt) cc_final: 0.6711 (tppt) REVERT: C 106 GLU cc_start: 0.5656 (tm-30) cc_final: 0.5192 (pp20) REVERT: C 109 ARG cc_start: 0.7915 (mpp-170) cc_final: 0.7504 (pmm150) outliers start: 44 outliers final: 22 residues processed: 118 average time/residue: 0.9877 time to fit residues: 128.8036 Evaluate side-chains 105 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 10994 Z= 0.475 Angle : 0.690 9.480 15001 Z= 0.350 Chirality : 0.048 0.456 1766 Planarity : 0.005 0.078 1824 Dihedral : 8.278 84.302 1894 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.90 % Allowed : 16.83 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1299 helix: 2.03 (0.20), residues: 695 sheet: -1.05 (0.46), residues: 125 loop : -1.55 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.010 0.001 HIS A 449 PHE 0.027 0.002 PHE A 302 TYR 0.022 0.002 TYR B 466 ARG 0.017 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 82 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8864 (tp40) cc_final: 0.7864 (tm-30) REVERT: B 112 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: B 159 TYR cc_start: 0.4017 (t80) cc_final: 0.3666 (t80) REVERT: B 277 GLU cc_start: 0.5474 (pt0) cc_final: 0.4586 (pt0) REVERT: B 278 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.3931 (mpt180) outliers start: 44 outliers final: 26 residues processed: 115 average time/residue: 0.9826 time to fit residues: 125.0626 Evaluate side-chains 106 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10994 Z= 0.197 Angle : 0.577 7.828 15001 Z= 0.293 Chirality : 0.042 0.377 1766 Planarity : 0.004 0.062 1824 Dihedral : 7.539 86.284 1894 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.75 % Allowed : 17.80 % Favored : 79.45 % 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: 0.87 (0.24), residues: 1299 helix: 2.22 (0.20), residues: 691 sheet: -0.89 (0.47), residues: 121 loop : -1.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 222 PHE 0.024 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.013 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8813 (tp40) cc_final: 0.7810 (tm-30) REVERT: B 112 GLN cc_start: 0.8682 (mt0) cc_final: 0.8306 (pt0) REVERT: B 159 TYR cc_start: 0.3888 (t80) cc_final: 0.3574 (t80) REVERT: B 277 GLU cc_start: 0.5615 (pt0) cc_final: 0.4720 (pt0) REVERT: B 278 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.3822 (mpt180) REVERT: C 96 LYS cc_start: 0.7144 (mttt) cc_final: 0.6738 (tppt) REVERT: C 183 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8404 (mm-30) outliers start: 31 outliers final: 17 residues processed: 108 average time/residue: 1.0559 time to fit residues: 125.4375 Evaluate side-chains 100 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10994 Z= 0.331 Angle : 0.634 8.863 15001 Z= 0.322 Chirality : 0.045 0.419 1766 Planarity : 0.005 0.061 1824 Dihedral : 7.555 87.642 1894 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.21 % Allowed : 18.51 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1299 helix: 2.16 (0.20), residues: 694 sheet: -1.03 (0.46), residues: 125 loop : -1.50 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.006 0.001 HIS A 449 PHE 0.026 0.001 PHE A 302 TYR 0.018 0.001 TYR B 466 ARG 0.013 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8848 (tp40) cc_final: 0.7924 (tm-30) REVERT: B 112 GLN cc_start: 0.8664 (mt0) cc_final: 0.8367 (pt0) REVERT: B 159 TYR cc_start: 0.3923 (t80) cc_final: 0.3596 (t80) REVERT: B 277 GLU cc_start: 0.5678 (pt0) cc_final: 0.4934 (pt0) REVERT: B 278 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.3953 (mpt180) REVERT: C 96 LYS cc_start: 0.7096 (mttt) cc_final: 0.6660 (tppt) REVERT: D 11 LYS cc_start: 0.8325 (mttp) cc_final: 0.8061 (mttt) outliers start: 25 outliers final: 20 residues processed: 102 average time/residue: 1.0428 time to fit residues: 117.2540 Evaluate side-chains 102 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10994 Z= 0.177 Angle : 0.571 7.437 15001 Z= 0.289 Chirality : 0.041 0.364 1766 Planarity : 0.004 0.053 1824 Dihedral : 7.040 89.642 1894 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.13 % Allowed : 18.69 % Favored : 79.19 % 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: 0.98 (0.24), residues: 1299 helix: 2.34 (0.20), residues: 684 sheet: -0.68 (0.46), residues: 123 loop : -1.52 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.013 0.001 TYR B 225 ARG 0.013 0.001 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8808 (tp40) cc_final: 0.7900 (tm-30) REVERT: B 112 GLN cc_start: 0.8685 (mt0) cc_final: 0.8407 (pt0) REVERT: B 159 TYR cc_start: 0.3838 (t80) cc_final: 0.3543 (t80) REVERT: B 385 ASP cc_start: 0.8933 (m-30) cc_final: 0.8716 (m-30) REVERT: C 96 LYS cc_start: 0.7055 (mttt) cc_final: 0.6681 (tppt) REVERT: C 183 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 24 outliers final: 19 residues processed: 104 average time/residue: 1.0376 time to fit residues: 118.8082 Evaluate side-chains 100 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.054949 restraints weight = 27904.808| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.50 r_work: 0.2714 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10994 Z= 0.369 Angle : 0.656 9.166 15001 Z= 0.333 Chirality : 0.046 0.427 1766 Planarity : 0.005 0.058 1824 Dihedral : 7.346 89.573 1894 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.39 % Allowed : 18.69 % Favored : 78.92 % 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: 0.81 (0.24), residues: 1299 helix: 2.14 (0.20), residues: 695 sheet: -1.00 (0.46), residues: 125 loop : -1.50 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.007 0.001 HIS A 449 PHE 0.024 0.002 PHE A 302 TYR 0.018 0.002 TYR B 466 ARG 0.013 0.001 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.37 seconds wall clock time: 61 minutes 47.18 seconds (3707.18 seconds total)