Starting phenix.real_space_refine on Wed Feb 14 02:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/02_2024/6kkr_0701.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 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-5238/modules/chem_data/mon_lib" Total number of atoms: 8416 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.36, per 1000 atoms: 0.64 Number of scatterers: 8416 At special positions: 0 Unit cell: (75.97, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 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=2.02 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=2.02 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 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: 52 helices and 4 sheets defined 71.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.753A 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 140 through 176 removed outlier: 7.052A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.721A 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 301 removed outlier: 3.661A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.679A 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 removed outlier: 3.623A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.593A 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: 4.405A 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 removed outlier: 3.545A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.893A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.753A 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 140 through 176 removed outlier: 7.052A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.721A 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 301 removed outlier: 3.661A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.679A 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 removed outlier: 3.623A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.593A 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: 4.405A 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 removed outlier: 3.545A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.893A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 650 " --> pdb=" O GLY B 646 " (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 329 496 hydrogen bonds defined for protein. 1416 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: 2.43 Time building geometry restraints manager: 4.17 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: 2320 1.47 - 1.60: 3728 1.60 - 1.73: 0 1.73 - 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: 95.96 - 103.64: 154 103.64 - 111.32: 3566 111.32 - 119.00: 3553 119.00 - 126.68: 4397 126.68 - 134.36: 124 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" C PRO B 230 " pdb=" N PRO B 231 " pdb=" CA PRO B 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C PRO A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C ILE A 571 " pdb=" N ALA A 572 " pdb=" CA ALA A 572 " ideal model delta sigma weight residual 122.40 128.23 -5.83 1.45e+00 4.76e-01 1.62e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5238 34.22 - 68.43: 52 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 A2000 " pdb=" C24 DU0 A2000 " pdb=" C25 DU0 A2000 " pdb=" O23 DU0 A2000 " 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 B2000 " pdb=" C24 DU0 B2000 " pdb=" C25 DU0 B2000 " pdb=" O23 DU0 B2000 " 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 - 0.083: 1252 0.083 - 0.167: 198 0.167 - 0.250: 12 0.250 - 0.333: 2 0.333 - 0.417: 2 Chirality restraints: 1466 Sorted by residual: 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 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 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 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 473 " 0.011 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE A 473 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 473 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 473 " -0.000 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 3176 2.91 - 3.46: 9098 3.46 - 4.02: 15205 4.02 - 4.58: 21610 4.58 - 5.14: 31161 Nonbonded interactions: 80250 Sorted by model distance: nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.348 2.440 nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.348 2.440 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 2.440 nonbonded pdb=" O2 GLC I 2 " pdb=" O4 GLC I 2 " model vdw 2.383 2.440 nonbonded pdb=" O GLU A 222 " pdb=" OG1 THR A 226 " model vdw 2.383 2.440 ... (remaining 80245 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.000 Extract box with map and model: 2.540 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.170 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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= 0.566 Angle : 1.123 10.401 11794 Z= 0.597 Chirality : 0.061 0.417 1466 Planarity : 0.007 0.063 1404 Dihedral : 18.504 171.079 3380 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.23 % Allowed : 2.38 % Favored : 97.39 % 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: -3.53 (0.20), residues: 1070 helix: -2.09 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 339 HIS 0.003 0.001 HIS B 394 PHE 0.036 0.004 PHE A 473 TYR 0.027 0.003 TYR B 466 ARG 0.006 0.001 ARG B 528 *********************** 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 244 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 0.867 Fit side-chains REVERT: A 400 ASP cc_start: 0.8009 (t0) cc_final: 0.7793 (t0) REVERT: A 405 LYS cc_start: 0.8314 (tttp) cc_final: 0.8078 (tttp) REVERT: A 449 LYS cc_start: 0.8156 (tttp) cc_final: 0.7754 (ttmt) REVERT: A 488 ASP cc_start: 0.8046 (m-30) cc_final: 0.7657 (m-30) REVERT: A 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7093 (mtp85) REVERT: B 400 ASP cc_start: 0.7975 (t0) cc_final: 0.7765 (t0) REVERT: B 405 LYS cc_start: 0.8302 (tttp) cc_final: 0.8065 (tttp) REVERT: B 449 LYS cc_start: 0.8152 (tttp) cc_final: 0.7744 (ttmt) REVERT: B 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7098 (mtp85) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 1.0641 time to fit residues: 277.4494 Evaluate side-chains 150 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 131 ASN A 347 ASN A 537 ASN A 615 HIS B 130 GLN B 131 ASN B 347 ASN B 537 ASN B 606 ASN B 615 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8626 Z= 0.197 Angle : 0.724 11.313 11794 Z= 0.330 Chirality : 0.059 1.031 1466 Planarity : 0.005 0.058 1404 Dihedral : 15.995 146.357 1650 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.20 % Allowed : 10.66 % 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: -1.14 (0.24), residues: 1070 helix: 0.12 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.001 0.001 HIS A 394 PHE 0.010 0.001 PHE A 427 TYR 0.013 0.001 TYR B 216 ARG 0.003 0.001 ARG B 317 *********************** 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 204 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 216 TYR cc_start: 0.8861 (m-10) cc_final: 0.8637 (m-80) REVERT: A 276 PHE cc_start: 0.7701 (m-10) cc_final: 0.7499 (m-10) REVERT: A 440 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7230 (mtt-85) REVERT: A 449 LYS cc_start: 0.8104 (tttp) cc_final: 0.7714 (ttmt) REVERT: A 612 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8093 (ttmp) REVERT: B 216 TYR cc_start: 0.8856 (m-10) cc_final: 0.8620 (m-80) REVERT: B 276 PHE cc_start: 0.7645 (m-10) cc_final: 0.7444 (m-10) REVERT: B 445 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7403 (mtm110) REVERT: B 449 LYS cc_start: 0.8102 (tttp) cc_final: 0.7685 (ttmt) REVERT: B 612 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8013 (ttmp) outliers start: 37 outliers final: 17 residues processed: 186 average time/residue: 1.1544 time to fit residues: 228.3891 Evaluate side-chains 160 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 612 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 0.0040 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 274 ASN A 337 GLN A 606 ASN B 131 ASN B 274 ASN B 337 GLN B 377 GLN B 606 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2631 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= 0.185 Angle : 0.630 9.496 11794 Z= 0.292 Chirality : 0.057 1.077 1466 Planarity : 0.004 0.050 1404 Dihedral : 13.053 143.604 1648 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.33 % Allowed : 10.20 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1070 helix: 1.05 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.001 0.000 HIS A 394 PHE 0.011 0.001 PHE A 428 TYR 0.010 0.001 TYR A 292 ARG 0.003 0.000 ARG A 440 *********************** 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 193 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 0.979 Fit side-chains REVERT: A 449 LYS cc_start: 0.8069 (tttp) cc_final: 0.7671 (ttmt) REVERT: A 496 VAL cc_start: 0.8613 (t) cc_final: 0.8398 (p) REVERT: B 445 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7416 (mtm110) outliers start: 47 outliers final: 26 residues processed: 171 average time/residue: 1.2129 time to fit residues: 220.5868 Evaluate side-chains 171 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2850 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= 0.184 Angle : 0.608 7.479 11794 Z= 0.287 Chirality : 0.045 0.666 1466 Planarity : 0.004 0.045 1404 Dihedral : 11.216 142.554 1648 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.33 % Allowed : 11.00 % 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: 0.42 (0.26), residues: 1070 helix: 1.50 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 547 PHE 0.011 0.001 PHE A 276 TYR 0.010 0.001 TYR A 292 ARG 0.006 0.000 ARG A 191 *********************** 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 196 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 349 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 349 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 445 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7428 (mtm110) outliers start: 47 outliers final: 25 residues processed: 174 average time/residue: 1.2161 time to fit residues: 225.0502 Evaluate side-chains 169 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8626 Z= 0.240 Angle : 0.640 8.506 11794 Z= 0.297 Chirality : 0.047 0.651 1466 Planarity : 0.004 0.043 1404 Dihedral : 10.472 143.939 1648 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.78 % Allowed : 11.00 % Favored : 83.22 % 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: 0.62 (0.26), residues: 1070 helix: 1.61 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.54 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS B 394 PHE 0.013 0.002 PHE B 428 TYR 0.012 0.001 TYR A 411 ARG 0.007 0.000 ARG A 191 *********************** 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 198 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7686 (t0) cc_final: 0.7345 (t0) REVERT: A 349 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8169 (p) REVERT: B 301 ASP cc_start: 0.7670 (t0) cc_final: 0.7336 (t0) REVERT: B 349 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 445 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7357 (mtm110) outliers start: 51 outliers final: 30 residues processed: 176 average time/residue: 1.1441 time to fit residues: 214.7095 Evaluate side-chains 175 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN B 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3127 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= 0.209 Angle : 0.631 10.026 11794 Z= 0.291 Chirality : 0.047 0.701 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.865 143.652 1648 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.90 % Allowed : 12.81 % Favored : 81.29 % 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 (0.26), residues: 1070 helix: 1.78 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE B 428 TYR 0.010 0.001 TYR A 292 ARG 0.006 0.000 ARG A 440 *********************** 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 197 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 145 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7672 (t0) cc_final: 0.7325 (t0) REVERT: A 349 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 440 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7368 (mmm-85) REVERT: A 484 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7271 (t0) REVERT: B 301 ASP cc_start: 0.7682 (t0) cc_final: 0.7334 (t0) REVERT: B 349 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8067 (p) REVERT: B 445 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7350 (mtm110) outliers start: 52 outliers final: 30 residues processed: 180 average time/residue: 1.1770 time to fit residues: 225.5641 Evaluate side-chains 176 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 319 GLN B 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8626 Z= 0.182 Angle : 0.605 8.664 11794 Z= 0.281 Chirality : 0.045 0.596 1466 Planarity : 0.004 0.041 1404 Dihedral : 8.662 141.627 1648 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.54 % Allowed : 15.65 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.18 (0.26), residues: 1070 helix: 2.07 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.37 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.001 0.000 HIS B 547 PHE 0.008 0.001 PHE B 428 TYR 0.009 0.001 TYR A 292 ARG 0.007 0.000 ARG A 191 *********************** 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 187 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7606 (t0) cc_final: 0.7293 (t0) REVERT: A 349 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 484 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7223 (t0) REVERT: B 301 ASP cc_start: 0.7622 (t0) cc_final: 0.7308 (t0) REVERT: B 349 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 445 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7496 (mtm110) outliers start: 40 outliers final: 26 residues processed: 174 average time/residue: 1.1124 time to fit residues: 206.6781 Evaluate side-chains 165 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR 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: 5.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8626 Z= 0.180 Angle : 0.601 8.490 11794 Z= 0.281 Chirality : 0.046 0.665 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.972 139.983 1648 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.65 % Allowed : 16.10 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.36 (0.26), residues: 1070 helix: 2.20 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.29 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE A 428 TYR 0.009 0.001 TYR A 292 ARG 0.008 0.000 ARG A 440 *********************** 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 178 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7626 (t0) cc_final: 0.7296 (t0) REVERT: A 349 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (p) REVERT: A 440 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7335 (mtm-85) REVERT: A 484 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7185 (t0) REVERT: B 301 ASP cc_start: 0.7640 (t0) cc_final: 0.7321 (t0) REVERT: B 349 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 445 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7493 (mtm110) outliers start: 41 outliers final: 28 residues processed: 165 average time/residue: 1.2133 time to fit residues: 212.7968 Evaluate side-chains 165 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 587 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 606 ASN B 319 GLN B 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8626 Z= 0.208 Angle : 0.603 8.425 11794 Z= 0.286 Chirality : 0.046 0.608 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.693 140.331 1648 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.31 % Allowed : 16.78 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.36 (0.26), residues: 1070 helix: 2.17 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.001 0.000 HIS A 547 PHE 0.010 0.001 PHE B 428 TYR 0.010 0.001 TYR A 411 ARG 0.006 0.001 ARG A 440 *********************** 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 179 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7627 (t0) cc_final: 0.7326 (t0) REVERT: A 349 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 440 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7440 (mmm-85) REVERT: A 484 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7295 (t0) REVERT: A 521 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 301 ASP cc_start: 0.7678 (t0) cc_final: 0.7356 (t0) REVERT: B 349 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 445 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7491 (mtm110) REVERT: B 484 ASP cc_start: 0.7734 (t0) cc_final: 0.7531 (t0) REVERT: B 521 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: B 647 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5913 (mtp) outliers start: 38 outliers final: 29 residues processed: 167 average time/residue: 1.2627 time to fit residues: 224.3234 Evaluate side-chains 173 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 647 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 606 ASN B 319 GLN B 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3513 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= 0.178 Angle : 0.585 8.256 11794 Z= 0.280 Chirality : 0.045 0.615 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.658 140.077 1648 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.31 % Allowed : 17.01 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1070 helix: 2.20 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 PHE 0.008 0.001 PHE B 211 TYR 0.009 0.001 TYR A 292 ARG 0.008 0.001 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 176 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7578 (t0) cc_final: 0.7297 (t0) REVERT: A 349 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 440 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7348 (mtm-85) REVERT: A 484 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7233 (t0) REVERT: A 521 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: B 301 ASP cc_start: 0.7638 (t0) cc_final: 0.7333 (t0) REVERT: B 349 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 445 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7475 (mtm110) REVERT: B 521 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: B 647 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.5848 (mtp) outliers start: 38 outliers final: 28 residues processed: 161 average time/residue: 1.2256 time to fit residues: 209.4854 Evaluate side-chains 169 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 647 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 319 GLN B 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098561 restraints weight = 9777.350| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.02 r_work: 0.2915 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8626 Z= 0.169 Angle : 0.578 8.168 11794 Z= 0.277 Chirality : 0.044 0.593 1466 Planarity : 0.004 0.049 1404 Dihedral : 7.361 138.680 1648 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.63 % Allowed : 17.91 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.61 (0.27), residues: 1070 helix: 2.32 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 PHE 0.008 0.001 PHE A 211 TYR 0.008 0.001 TYR A 292 ARG 0.013 0.001 ARG A 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3714.28 seconds wall clock time: 66 minutes 27.56 seconds (3987.56 seconds total)