Starting phenix.real_space_refine on Mon Mar 11 13:49:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kku_0703/03_2024/6kku_0703.pdb" } resolution = 3.5 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= 0.003 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 S 68 5.16 5 Cl 2 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8412 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" 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: "D" 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: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' CL': 1, 'DU0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' CL': 1, 'DU0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.29, per 1000 atoms: 0.63 Number of scatterers: 8412 At special positions: 0 Unit cell: (78.11, 101.65, 102.72, 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) Cl 2 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " 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=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 69.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.916A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 176 removed outlier: 7.212A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.977A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.522A pdb=" N GLY A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.589A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.526A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.567A pdb=" N ASN A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.565A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.908A pdb=" N SER A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.650A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.633A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.686A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.178A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 536 Proline residue: A 527 - end of helix removed outlier: 3.540A pdb=" N ASP A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.406A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.895A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix removed outlier: 3.751A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.741A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.508A pdb=" N ALA A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.916A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 176 removed outlier: 7.212A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.976A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.522A pdb=" N GLY B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.589A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 298 Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.566A pdb=" N ASN B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.566A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.908A pdb=" N SER B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.649A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.632A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.686A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.179A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 536 Proline residue: B 527 - end of helix removed outlier: 3.539A pdb=" N ASP B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.405A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.895A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix removed outlier: 3.751A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.740A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.508A pdb=" N ALA B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329 486 hydrogen bonds defined for protein. 1386 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: 2.35 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.47: 2313 1.47 - 1.60: 3735 1.60 - 1.72: 0 1.72 - 1.85: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BGC J 1 " pdb=" O5 BGC J 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.402 1.485 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 95.08 - 102.87: 54 102.87 - 110.65: 3005 110.65 - 118.43: 3871 118.43 - 126.22: 4726 126.22 - 134.00: 138 Bond angle restraints: 11794 Sorted by residual: angle pdb=" CA PRO A 230 " pdb=" C PRO A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 117.93 122.96 -5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA PRO B 230 " pdb=" C PRO B 230 " pdb=" N PRO B 231 " ideal model delta sigma weight residual 117.93 122.90 -4.97 1.20e+00 6.94e-01 1.72e+01 angle pdb=" N VAL A 490 " pdb=" CA VAL A 490 " pdb=" C VAL A 490 " ideal model delta sigma weight residual 106.53 111.67 -5.14 1.41e+00 5.03e-01 1.33e+01 angle pdb=" N PHE A 428 " pdb=" CA PHE A 428 " pdb=" C PHE A 428 " ideal model delta sigma weight residual 113.16 118.28 -5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" N PHE B 428 " pdb=" CA PHE B 428 " pdb=" C PHE B 428 " ideal model delta sigma weight residual 113.16 118.28 -5.12 1.42e+00 4.96e-01 1.30e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5236 34.22 - 68.43: 54 68.43 - 102.65: 42 102.65 - 136.86: 32 136.86 - 171.08: 2 Dihedral angle restraints: 5366 sinusoidal: 2284 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A1106 " pdb=" C24 DU0 A1106 " pdb=" C25 DU0 A1106 " pdb=" O23 DU0 A1106 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C26 DU0 B1108 " pdb=" C24 DU0 B1108 " pdb=" C25 DU0 B1108 " pdb=" O23 DU0 B1108 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sinusoidal sigma weight residual 60.18 -167.16 -132.66 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1212 0.080 - 0.160: 237 0.160 - 0.240: 15 0.240 - 0.319: 0 0.319 - 0.399: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 312 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 GLC F 2 " pdb=" O4 BGC F 1 " pdb=" C2 GLC F 2 " pdb=" O5 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.68e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO B 409 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO A 409 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 467 " -0.016 2.00e-02 2.50e+03 1.66e-02 4.81e+00 pdb=" CG PHE A 467 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 467 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 467 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 467 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 467 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 467 " -0.001 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1782 2.77 - 3.31: 7841 3.31 - 3.84: 13265 3.84 - 4.37: 14998 4.37 - 4.90: 26580 Nonbonded interactions: 64466 Sorted by model distance: nonbonded pdb=" OH TYR A 292 " pdb=" OG SER A 468 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR B 292 " pdb=" OG SER B 468 " model vdw 2.244 2.440 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.344 2.440 nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.345 2.440 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 2.440 ... (remaining 64461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.490 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: 2.530 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.460 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.009 0.088 8626 Z= 0.595 Angle : 1.082 9.734 11794 Z= 0.540 Chirality : 0.061 0.399 1466 Planarity : 0.008 0.071 1404 Dihedral : 18.283 171.079 3380 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.21), residues: 1070 helix: -1.68 (0.16), residues: 622 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 339 HIS 0.006 0.001 HIS B 615 PHE 0.039 0.004 PHE A 467 TYR 0.025 0.003 TYR A 292 ARG 0.004 0.001 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 0.949 Fit side-chains REVERT: A 180 VAL cc_start: 0.8404 (t) cc_final: 0.8169 (t) REVERT: A 297 LYS cc_start: 0.8588 (tttm) cc_final: 0.7946 (mmtm) REVERT: A 405 LYS cc_start: 0.8370 (tttp) cc_final: 0.7862 (ttpp) REVERT: B 144 MET cc_start: 0.8255 (ttm) cc_final: 0.7995 (ttt) REVERT: B 176 THR cc_start: 0.8818 (p) cc_final: 0.8435 (t) REVERT: B 297 LYS cc_start: 0.8699 (tttm) cc_final: 0.7868 (mmtm) REVERT: B 405 LYS cc_start: 0.8357 (tttp) cc_final: 0.7864 (ttpp) REVERT: B 484 ASP cc_start: 0.8380 (m-30) cc_final: 0.8071 (m-30) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2185 time to fit residues: 84.9132 Evaluate side-chains 141 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 531 GLN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8626 Z= 0.176 Angle : 0.691 9.070 11794 Z= 0.322 Chirality : 0.043 0.210 1466 Planarity : 0.005 0.067 1404 Dihedral : 15.410 151.693 1648 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.93 % Allowed : 10.77 % Favored : 87.30 % 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: -0.95 (0.24), residues: 1070 helix: 0.59 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 616 HIS 0.002 0.001 HIS B 615 PHE 0.013 0.001 PHE B 467 TYR 0.017 0.001 TYR A 613 ARG 0.004 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 0.972 Fit side-chains REVERT: A 118 MET cc_start: 0.6990 (mmt) cc_final: 0.6790 (mmt) REVERT: A 144 MET cc_start: 0.8049 (ttm) cc_final: 0.7624 (ttt) REVERT: A 297 LYS cc_start: 0.8650 (tttm) cc_final: 0.7983 (mmtm) REVERT: A 405 LYS cc_start: 0.8101 (tttp) cc_final: 0.7662 (ttpp) REVERT: A 531 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: A 537 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8295 (t0) REVERT: A 614 TYR cc_start: 0.7840 (t80) cc_final: 0.7396 (t80) REVERT: B 130 GLN cc_start: 0.8120 (tt0) cc_final: 0.7782 (tt0) REVERT: B 144 MET cc_start: 0.8043 (ttm) cc_final: 0.7765 (ttt) REVERT: B 297 LYS cc_start: 0.8764 (tttm) cc_final: 0.7904 (mmtm) REVERT: B 380 LEU cc_start: 0.8787 (mt) cc_final: 0.8404 (mt) REVERT: B 405 LYS cc_start: 0.8005 (tttp) cc_final: 0.7586 (ttpp) REVERT: B 490 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7988 (p) REVERT: B 537 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8117 (t0) outliers start: 17 outliers final: 6 residues processed: 185 average time/residue: 0.1805 time to fit residues: 47.6623 Evaluate side-chains 150 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8626 Z= 0.197 Angle : 0.639 10.000 11794 Z= 0.308 Chirality : 0.044 0.294 1466 Planarity : 0.004 0.053 1404 Dihedral : 12.673 146.652 1648 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.83 % Allowed : 12.02 % Favored : 85.15 % 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 (0.26), residues: 1070 helix: 1.33 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 616 HIS 0.005 0.001 HIS A 615 PHE 0.027 0.001 PHE B 261 TYR 0.016 0.001 TYR B 613 ARG 0.004 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8149 (ttm) cc_final: 0.7887 (ttm) REVERT: A 405 LYS cc_start: 0.8040 (tttp) cc_final: 0.7627 (ttpp) REVERT: B 130 GLN cc_start: 0.8115 (tt0) cc_final: 0.7772 (tt0) REVERT: B 251 MET cc_start: 0.8678 (mmm) cc_final: 0.8437 (mtp) REVERT: B 380 LEU cc_start: 0.8794 (mt) cc_final: 0.8481 (mt) REVERT: B 405 LYS cc_start: 0.7917 (tttp) cc_final: 0.7534 (ttpp) REVERT: B 410 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8220 (tt) REVERT: B 537 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8255 (t0) outliers start: 25 outliers final: 11 residues processed: 174 average time/residue: 0.1778 time to fit residues: 44.2001 Evaluate side-chains 147 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8626 Z= 0.227 Angle : 0.646 7.433 11794 Z= 0.307 Chirality : 0.044 0.250 1466 Planarity : 0.004 0.046 1404 Dihedral : 10.899 143.585 1648 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 13.83 % Favored : 83.67 % 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: 0.44 (0.26), residues: 1070 helix: 1.85 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 616 HIS 0.003 0.001 HIS A 615 PHE 0.013 0.001 PHE B 428 TYR 0.017 0.001 TYR B 613 ARG 0.003 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8245 (ttm) cc_final: 0.7951 (ttm) REVERT: B 130 GLN cc_start: 0.8092 (tt0) cc_final: 0.7791 (tt0) REVERT: B 380 LEU cc_start: 0.8775 (mt) cc_final: 0.8477 (mt) REVERT: B 405 LYS cc_start: 0.7934 (tttp) cc_final: 0.7563 (ttpp) REVERT: B 410 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8376 (tt) outliers start: 22 outliers final: 15 residues processed: 158 average time/residue: 0.1757 time to fit residues: 39.7749 Evaluate side-chains 153 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 chunk 87 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0760 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8626 Z= 0.189 Angle : 0.630 7.919 11794 Z= 0.298 Chirality : 0.043 0.231 1466 Planarity : 0.004 0.043 1404 Dihedral : 10.159 142.186 1648 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.61 % Allowed : 14.85 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1070 helix: 2.03 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 616 HIS 0.003 0.001 HIS B 615 PHE 0.011 0.001 PHE A 428 TYR 0.015 0.001 TYR B 613 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.955 Fit side-chains REVERT: A 144 MET cc_start: 0.8241 (ttm) cc_final: 0.7832 (ttt) REVERT: A 594 LEU cc_start: 0.9069 (tp) cc_final: 0.8796 (tp) REVERT: B 130 GLN cc_start: 0.8110 (tt0) cc_final: 0.7772 (tt0) REVERT: B 262 MET cc_start: 0.8285 (mtm) cc_final: 0.8031 (mtt) REVERT: B 380 LEU cc_start: 0.8765 (mt) cc_final: 0.8480 (mt) REVERT: B 405 LYS cc_start: 0.7929 (tttp) cc_final: 0.7553 (ttpp) REVERT: B 410 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 594 LEU cc_start: 0.9075 (tp) cc_final: 0.8778 (tp) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.1740 time to fit residues: 40.6311 Evaluate side-chains 151 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8626 Z= 0.191 Angle : 0.641 8.345 11794 Z= 0.302 Chirality : 0.043 0.227 1466 Planarity : 0.004 0.040 1404 Dihedral : 9.262 142.731 1648 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.51 % Allowed : 14.74 % Favored : 81.75 % 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: 0.80 (0.26), residues: 1070 helix: 2.14 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 616 HIS 0.003 0.001 HIS A 615 PHE 0.012 0.001 PHE A 428 TYR 0.016 0.001 TYR B 613 ARG 0.001 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8010 (tt0) cc_final: 0.7774 (tt0) REVERT: A 144 MET cc_start: 0.8198 (ttm) cc_final: 0.7804 (ttt) REVERT: A 594 LEU cc_start: 0.9063 (tp) cc_final: 0.8804 (tt) REVERT: B 130 GLN cc_start: 0.8173 (tt0) cc_final: 0.7844 (tt0) REVERT: B 380 LEU cc_start: 0.8751 (mt) cc_final: 0.8473 (mt) REVERT: B 405 LYS cc_start: 0.7879 (tttp) cc_final: 0.7525 (ttpp) REVERT: B 594 LEU cc_start: 0.9079 (tp) cc_final: 0.8814 (tt) outliers start: 31 outliers final: 19 residues processed: 168 average time/residue: 0.1780 time to fit residues: 43.3065 Evaluate side-chains 158 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8626 Z= 0.174 Angle : 0.638 8.355 11794 Z= 0.301 Chirality : 0.043 0.217 1466 Planarity : 0.004 0.040 1404 Dihedral : 8.517 141.859 1648 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.27 % Allowed : 15.99 % Favored : 81.75 % 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: 0.96 (0.26), residues: 1070 helix: 2.26 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.02 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 616 HIS 0.004 0.001 HIS B 615 PHE 0.011 0.001 PHE B 261 TYR 0.015 0.001 TYR B 613 ARG 0.002 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8020 (tt0) cc_final: 0.7747 (tt0) REVERT: A 144 MET cc_start: 0.8167 (ttm) cc_final: 0.7866 (ttt) REVERT: A 594 LEU cc_start: 0.9045 (tp) cc_final: 0.8803 (tt) REVERT: B 130 GLN cc_start: 0.8106 (tt0) cc_final: 0.7814 (tt0) REVERT: B 380 LEU cc_start: 0.8741 (mt) cc_final: 0.8458 (mt) REVERT: B 405 LYS cc_start: 0.7850 (tttp) cc_final: 0.7495 (ttpp) REVERT: B 594 LEU cc_start: 0.9056 (tp) cc_final: 0.8810 (tt) REVERT: B 647 MET cc_start: 0.8363 (ttp) cc_final: 0.8143 (ttp) outliers start: 20 outliers final: 16 residues processed: 165 average time/residue: 0.1779 time to fit residues: 42.6539 Evaluate side-chains 157 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8626 Z= 0.171 Angle : 0.638 9.077 11794 Z= 0.300 Chirality : 0.042 0.211 1466 Planarity : 0.004 0.039 1404 Dihedral : 7.751 140.804 1648 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 16.55 % Favored : 81.07 % 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: 1.11 (0.26), residues: 1070 helix: 2.27 (0.21), residues: 650 sheet: 1.73 (1.09), residues: 20 loop : -2.11 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 616 HIS 0.003 0.000 HIS B 615 PHE 0.010 0.001 PHE B 428 TYR 0.015 0.001 TYR B 613 ARG 0.002 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8057 (tt0) cc_final: 0.7783 (tt0) REVERT: A 144 MET cc_start: 0.8070 (ttm) cc_final: 0.7813 (ttt) REVERT: A 594 LEU cc_start: 0.9045 (tp) cc_final: 0.8801 (tt) REVERT: B 130 GLN cc_start: 0.8101 (tt0) cc_final: 0.7791 (tt0) REVERT: B 380 LEU cc_start: 0.8749 (mt) cc_final: 0.8456 (mt) REVERT: B 405 LYS cc_start: 0.7856 (tttp) cc_final: 0.7484 (ttpp) REVERT: B 594 LEU cc_start: 0.9051 (tp) cc_final: 0.8813 (tt) outliers start: 21 outliers final: 17 residues processed: 161 average time/residue: 0.1820 time to fit residues: 42.1672 Evaluate side-chains 157 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8626 Z= 0.176 Angle : 0.651 9.830 11794 Z= 0.309 Chirality : 0.043 0.219 1466 Planarity : 0.004 0.038 1404 Dihedral : 7.384 140.396 1648 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.27 % Allowed : 16.67 % Favored : 81.07 % 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: 1.14 (0.26), residues: 1070 helix: 2.27 (0.21), residues: 650 sheet: 1.69 (1.09), residues: 20 loop : -2.03 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.002 0.000 HIS A 615 PHE 0.011 0.001 PHE A 541 TYR 0.015 0.001 TYR A 613 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8079 (tt0) cc_final: 0.7782 (tt0) REVERT: A 144 MET cc_start: 0.8073 (ttm) cc_final: 0.7836 (ttt) REVERT: A 594 LEU cc_start: 0.9034 (tp) cc_final: 0.8806 (tt) REVERT: B 130 GLN cc_start: 0.8093 (tt0) cc_final: 0.7850 (tt0) REVERT: B 380 LEU cc_start: 0.8747 (mt) cc_final: 0.8463 (mt) REVERT: B 405 LYS cc_start: 0.7824 (tttp) cc_final: 0.7450 (ttpp) REVERT: B 594 LEU cc_start: 0.9061 (tp) cc_final: 0.8837 (tt) outliers start: 20 outliers final: 15 residues processed: 163 average time/residue: 0.1767 time to fit residues: 41.4408 Evaluate side-chains 158 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8626 Z= 0.181 Angle : 0.669 12.071 11794 Z= 0.313 Chirality : 0.043 0.255 1466 Planarity : 0.004 0.038 1404 Dihedral : 7.231 140.687 1648 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.04 % Allowed : 17.23 % Favored : 80.73 % 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: 1.20 (0.27), residues: 1070 helix: 2.31 (0.21), residues: 650 sheet: 1.72 (1.08), residues: 20 loop : -1.99 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.002 0.000 HIS A 615 PHE 0.012 0.001 PHE A 541 TYR 0.015 0.001 TYR A 613 ARG 0.002 0.000 ARG A 445 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8006 (tt0) cc_final: 0.7769 (tt0) REVERT: A 144 MET cc_start: 0.8079 (ttm) cc_final: 0.7845 (ttt) REVERT: B 130 GLN cc_start: 0.8137 (tt0) cc_final: 0.7837 (tt0) REVERT: B 380 LEU cc_start: 0.8751 (mt) cc_final: 0.8472 (mt) REVERT: B 405 LYS cc_start: 0.7806 (tttp) cc_final: 0.7464 (ttpp) REVERT: B 594 LEU cc_start: 0.9062 (tp) cc_final: 0.8829 (tt) outliers start: 18 outliers final: 15 residues processed: 155 average time/residue: 0.1730 time to fit residues: 38.4461 Evaluate side-chains 156 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** 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 = 0.3650 r_free = 0.3650 target = 0.137214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113491 restraints weight = 13595.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116786 restraints weight = 7703.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118864 restraints weight = 5458.260| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8626 Z= 0.169 Angle : 0.665 10.902 11794 Z= 0.312 Chirality : 0.043 0.268 1466 Planarity : 0.004 0.038 1404 Dihedral : 7.129 140.712 1648 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.81 % Allowed : 17.80 % Favored : 80.39 % 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: 1.32 (0.27), residues: 1070 helix: 2.41 (0.21), residues: 636 sheet: 1.73 (1.08), residues: 20 loop : -1.79 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.002 0.000 HIS A 615 PHE 0.015 0.001 PHE B 261 TYR 0.015 0.001 TYR B 613 ARG 0.003 0.000 ARG B 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.99 seconds wall clock time: 33 minutes 0.79 seconds (1980.79 seconds total)