Starting phenix.real_space_refine on Fri Mar 15 20:12:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tth_26115/03_2024/7tth_26115.pdb" } resolution = 3.25 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= 0.114 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 K 2 8.98 5 S 82 5.16 5 C 8296 2.51 5 N 2114 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 333 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.58 Number of scatterers: 12698 At special positions: 0 Unit cell: (114.66, 95.004, 149.604, 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) K 2 19.00 S 82 16.00 O 2204 8.00 N 2114 7.00 C 8296 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=2.04 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=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 58.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.965A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 198 through 227 removed outlier: 3.726A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 269 removed outlier: 4.319A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.067A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.523A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.800A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.568A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 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 433 through 437 Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.927A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.542A pdb=" N GLY A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 503 through 537 removed outlier: 4.245A pdb=" N ILE A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.976A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.562A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 666 through 680 removed outlier: 3.651A pdb=" N ALA A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.756A pdb=" N LEU A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.796A pdb=" N ILE A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 4.206A pdb=" N GLN A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.922A pdb=" N THR A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 854 through 859 removed outlier: 3.859A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 859' Processing helix chain 'A' and resid 860 through 867 removed outlier: 4.115A pdb=" N GLN A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.790A pdb=" N LYS A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1034 removed outlier: 3.947A pdb=" N VAL A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A1028 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 4.287A pdb=" N GLU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1062 " --> pdb=" O GLU A1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.999A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 198 through 227 removed outlier: 3.755A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 269 removed outlier: 4.130A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 298 removed outlier: 4.043A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.516A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.697A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.587A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 419 through 428 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 433 through 439 removed outlier: 3.518A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.934A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.507A pdb=" N GLY B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 488' Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 503 through 537 removed outlier: 4.317A pdb=" N ILE B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 543 through 547 removed outlier: 3.849A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 570 Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.530A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.559A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 666 through 680 removed outlier: 3.637A pdb=" N ALA B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 3.778A pdb=" N LEU B 712 " --> pdb=" O TYR B 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.504A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 756 " --> pdb=" O MET B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 removed outlier: 4.201A pdb=" N GLN B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 821 removed outlier: 3.774A pdb=" N THR B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.839A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B 859 " --> pdb=" O GLY B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 859' Processing helix chain 'B' and resid 860 through 867 removed outlier: 4.117A pdb=" N GLN B 867 " --> pdb=" O PHE B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 874 removed outlier: 4.323A pdb=" N LYS B 873 " --> pdb=" O VAL B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.588A pdb=" N LYS B 893 " --> pdb=" O ILE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1034 removed outlier: 3.905A pdb=" N VAL B1023 " --> pdb=" O MET B1019 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B1028 " --> pdb=" O LYS B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 4.460A pdb=" N GLU B1061 " --> pdb=" O MET B1057 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1062 " --> pdb=" O GLU B1058 " (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 'A' and resid 761 through 767 removed outlier: 6.511A pdb=" N THR A 725 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 763 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 727 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 765 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 729 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 767 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE A 731 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 694 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY A 728 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 696 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL A 730 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TRP A 849 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 767 removed outlier: 6.382A pdb=" N THR B 725 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 763 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 727 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL B 765 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER B 729 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA B 767 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 731 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 694 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY B 728 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 696 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL B 730 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 695 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N TRP B 849 " --> pdb=" O ASN B1042 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 2052 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: 4.23 Time building geometry restraints manager: 5.56 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: 3956 1.35 - 1.47: 3367 1.47 - 1.60: 5549 1.60 - 1.72: 0 1.72 - 1.85: 124 Bond restraints: 12996 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.568 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " ideal model delta sigma weight residual 1.532 1.594 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 12991 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 400 106.51 - 113.39: 7267 113.39 - 120.28: 4533 120.28 - 127.16: 5428 127.16 - 134.04: 164 Bond angle restraints: 17792 Sorted by residual: angle pdb=" CA LEU B 410 " pdb=" CB LEU B 410 " pdb=" CG LEU B 410 " ideal model delta sigma weight residual 116.30 128.36 -12.06 3.50e+00 8.16e-02 1.19e+01 angle pdb=" CA LEU A 410 " pdb=" CB LEU A 410 " pdb=" CG LEU A 410 " ideal model delta sigma weight residual 116.30 128.28 -11.98 3.50e+00 8.16e-02 1.17e+01 angle pdb=" C LEU A 625 " pdb=" N CYS A 626 " pdb=" CA CYS A 626 " ideal model delta sigma weight residual 122.38 116.31 6.07 1.81e+00 3.05e-01 1.13e+01 angle pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sigma weight residual 113.21 123.27 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C LEU B 625 " pdb=" N CYS B 626 " pdb=" CA CYS B 626 " ideal model delta sigma weight residual 122.38 116.39 5.99 1.81e+00 3.05e-01 1.09e+01 ... (remaining 17787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 7293 22.82 - 45.64: 299 45.64 - 68.46: 41 68.46 - 91.28: 11 91.28 - 114.10: 6 Dihedral angle restraints: 7650 sinusoidal: 2628 harmonic: 5022 Sorted by residual: dihedral pdb=" CA CYS B 626 " pdb=" C CYS B 626 " pdb=" N LEU B 627 " pdb=" CA LEU B 627 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 50.50 42.50 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 7647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2072 0.091 - 0.182: 105 0.182 - 0.273: 4 0.273 - 0.365: 0 0.365 - 0.456: 1 Chirality restraints: 2182 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 361 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA CYS B 626 " pdb=" N CYS B 626 " pdb=" C CYS B 626 " pdb=" CB CYS B 626 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2179 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 626 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C CYS B 626 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS B 626 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 627 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 626 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C CYS A 626 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS A 626 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 627 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 539 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 540 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 540 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 540 " -0.024 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3668 2.81 - 3.40: 14430 3.40 - 3.98: 21980 3.98 - 4.56: 29989 4.56 - 5.14: 44539 Nonbonded interactions: 114606 Sorted by model distance: nonbonded pdb=" OG1 THR B 604 " pdb=" NH1 ARG B 679 " model vdw 2.232 2.520 nonbonded pdb=" O GLY B 517 " pdb=" NE2 GLN B 521 " model vdw 2.239 2.520 nonbonded pdb=" O GLY A 517 " pdb=" NE2 GLN A 521 " model vdw 2.253 2.520 nonbonded pdb=" OE1 GLN A 599 " pdb=" OG1 THR A 604 " model vdw 2.261 2.440 nonbonded pdb=" O ALA A 399 " pdb=" O6 NAG C 1 " model vdw 2.274 2.440 ... (remaining 114601 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 'E' selection = chain 'F' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 4.310 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 37.320 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.004 0.162 12996 Z= 0.241 Angle : 0.705 12.063 17792 Z= 0.377 Chirality : 0.046 0.456 2182 Planarity : 0.004 0.043 2194 Dihedral : 13.053 114.098 4416 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1742 helix: 1.66 (0.18), residues: 862 sheet: -0.66 (0.45), residues: 142 loop : -2.00 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 556 HIS 0.003 0.001 HIS A 788 PHE 0.016 0.001 PHE A 591 TYR 0.013 0.001 TYR B 216 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6054 (Cg_exo) cc_final: 0.5843 (Cg_endo) REVERT: A 478 GLU cc_start: 0.6811 (pm20) cc_final: 0.6497 (pm20) REVERT: A 484 ASP cc_start: 0.7610 (t0) cc_final: 0.7166 (t0) REVERT: A 556 TRP cc_start: 0.7055 (m-90) cc_final: 0.6762 (m100) REVERT: A 1042 ASN cc_start: 0.7189 (t0) cc_final: 0.6852 (m-40) REVERT: A 1059 PHE cc_start: 0.4331 (p90) cc_final: 0.3508 (m-80) REVERT: B 312 ASN cc_start: 0.7680 (t0) cc_final: 0.7378 (t0) REVERT: B 484 ASP cc_start: 0.7566 (t0) cc_final: 0.7258 (t0) REVERT: B 1059 PHE cc_start: 0.4312 (p90) cc_final: 0.3800 (m-80) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2419 time to fit residues: 86.0682 Evaluate side-chains 167 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.0670 chunk 73 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 521 GLN A 537 ASN B 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12996 Z= 0.188 Angle : 0.621 11.731 17792 Z= 0.302 Chirality : 0.044 0.404 2182 Planarity : 0.004 0.034 2194 Dihedral : 7.699 101.044 2030 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.25 % Allowed : 7.74 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.29 (0.21), residues: 1742 helix: 1.84 (0.18), residues: 878 sheet: -0.65 (0.44), residues: 146 loop : -1.81 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 690 HIS 0.004 0.001 HIS A 344 PHE 0.018 0.001 PHE A1059 TYR 0.012 0.001 TYR B1056 ARG 0.004 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6080 (Cg_exo) cc_final: 0.5851 (Cg_endo) REVERT: A 484 ASP cc_start: 0.7691 (t0) cc_final: 0.7216 (t0) REVERT: A 556 TRP cc_start: 0.6765 (m-90) cc_final: 0.6481 (m100) REVERT: A 771 ARG cc_start: 0.7184 (ptp90) cc_final: 0.6923 (ptp90) REVERT: A 1042 ASN cc_start: 0.7336 (t0) cc_final: 0.6852 (m-40) REVERT: A 1059 PHE cc_start: 0.4563 (p90) cc_final: 0.3761 (m-80) REVERT: B 312 ASN cc_start: 0.7880 (t0) cc_final: 0.7419 (t0) REVERT: B 448 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: B 484 ASP cc_start: 0.7745 (t0) cc_final: 0.7417 (t0) REVERT: B 553 GLU cc_start: 0.7013 (tt0) cc_final: 0.6783 (tt0) REVERT: B 1059 PHE cc_start: 0.4552 (p90) cc_final: 0.3775 (m-80) outliers start: 15 outliers final: 5 residues processed: 188 average time/residue: 0.2038 time to fit residues: 58.2679 Evaluate side-chains 165 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12996 Z= 0.251 Angle : 0.639 14.909 17792 Z= 0.309 Chirality : 0.046 0.487 2182 Planarity : 0.004 0.035 2194 Dihedral : 6.930 98.394 2030 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.91 % Allowed : 10.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.25 (0.20), residues: 1742 helix: 1.71 (0.18), residues: 878 sheet: 0.43 (0.47), residues: 116 loop : -1.86 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.002 PHE B1059 TYR 0.013 0.001 TYR B 384 ARG 0.006 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 484 ASP cc_start: 0.7820 (t0) cc_final: 0.7351 (t0) REVERT: A 587 MET cc_start: 0.7380 (tpt) cc_final: 0.6917 (tpp) REVERT: A 1059 PHE cc_start: 0.4806 (p90) cc_final: 0.3289 (m-80) REVERT: B 312 ASN cc_start: 0.8063 (t0) cc_final: 0.7563 (t0) REVERT: B 484 ASP cc_start: 0.7790 (t0) cc_final: 0.7440 (t0) REVERT: B 536 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6596 (t0) REVERT: B 587 MET cc_start: 0.7331 (tpt) cc_final: 0.6997 (tpt) REVERT: B 1059 PHE cc_start: 0.4916 (p90) cc_final: 0.3485 (m-80) outliers start: 23 outliers final: 15 residues processed: 181 average time/residue: 0.2125 time to fit residues: 58.4346 Evaluate side-chains 170 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 850 TRP Chi-restraints excluded: chain B residue 1080 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12996 Z= 0.196 Angle : 0.591 9.526 17792 Z= 0.286 Chirality : 0.044 0.482 2182 Planarity : 0.004 0.031 2194 Dihedral : 6.557 95.500 2030 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.16 % Allowed : 12.15 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.40 (0.21), residues: 1742 helix: 1.86 (0.18), residues: 882 sheet: -0.56 (0.43), residues: 146 loop : -1.69 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE B1059 TYR 0.010 0.001 TYR B 292 ARG 0.006 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5442 (tt) REVERT: A 448 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: A 484 ASP cc_start: 0.7805 (t0) cc_final: 0.7393 (t0) REVERT: A 587 MET cc_start: 0.7255 (tpt) cc_final: 0.6876 (tpp) REVERT: A 1059 PHE cc_start: 0.5139 (p90) cc_final: 0.3416 (m-80) REVERT: B 484 ASP cc_start: 0.7729 (t0) cc_final: 0.7449 (t0) REVERT: B 536 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6689 (t0) REVERT: B 587 MET cc_start: 0.7175 (tpt) cc_final: 0.6809 (tpp) REVERT: B 1059 PHE cc_start: 0.4940 (p90) cc_final: 0.3473 (m-80) outliers start: 26 outliers final: 13 residues processed: 179 average time/residue: 0.2202 time to fit residues: 59.8136 Evaluate side-chains 167 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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: 0.6914 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12996 Z= 0.211 Angle : 0.591 10.002 17792 Z= 0.289 Chirality : 0.044 0.489 2182 Planarity : 0.004 0.033 2194 Dihedral : 6.331 92.077 2030 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.41 % Allowed : 13.23 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.51 (0.21), residues: 1742 helix: 1.94 (0.18), residues: 882 sheet: 0.43 (0.44), residues: 116 loop : -1.78 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 PHE 0.020 0.001 PHE B1059 TYR 0.010 0.001 TYR A 292 ARG 0.006 0.000 ARG B 771 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5294 (tt) REVERT: A 484 ASP cc_start: 0.7812 (t0) cc_final: 0.7439 (t0) REVERT: A 587 MET cc_start: 0.7269 (tpt) cc_final: 0.6881 (tpp) REVERT: A 1059 PHE cc_start: 0.5470 (p90) cc_final: 0.3378 (m-80) REVERT: B 251 MET cc_start: 0.5090 (mtt) cc_final: 0.4821 (mtt) REVERT: B 484 ASP cc_start: 0.7651 (t0) cc_final: 0.7376 (t0) REVERT: B 536 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6566 (t0) REVERT: B 587 MET cc_start: 0.7130 (tpt) cc_final: 0.6771 (tpp) REVERT: B 1059 PHE cc_start: 0.5174 (p90) cc_final: 0.3403 (m-80) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.2105 time to fit residues: 58.8511 Evaluate side-chains 175 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 850 TRP Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12996 Z= 0.226 Angle : 0.596 10.335 17792 Z= 0.292 Chirality : 0.044 0.490 2182 Planarity : 0.004 0.034 2194 Dihedral : 6.148 87.644 2030 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.91 % Allowed : 14.81 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.50 (0.21), residues: 1742 helix: 1.94 (0.17), residues: 884 sheet: 0.22 (0.43), residues: 120 loop : -1.77 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.004 0.001 HIS A 344 PHE 0.020 0.001 PHE B1059 TYR 0.010 0.001 TYR B 466 ARG 0.006 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5195 (tt) REVERT: A 484 ASP cc_start: 0.7842 (t0) cc_final: 0.7505 (t0) REVERT: A 587 MET cc_start: 0.7274 (tpt) cc_final: 0.6897 (tpp) REVERT: A 808 TRP cc_start: 0.5751 (p-90) cc_final: 0.5447 (p-90) REVERT: A 1059 PHE cc_start: 0.5373 (p90) cc_final: 0.3149 (m-80) REVERT: B 251 MET cc_start: 0.5131 (mtt) cc_final: 0.4924 (mtt) REVERT: B 410 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5017 (tt) REVERT: B 484 ASP cc_start: 0.7704 (t0) cc_final: 0.7397 (t0) REVERT: B 536 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6834 (t0) REVERT: B 587 MET cc_start: 0.7158 (tpt) cc_final: 0.6806 (tpp) REVERT: B 808 TRP cc_start: 0.5531 (p-90) cc_final: 0.5222 (p-90) REVERT: B 1059 PHE cc_start: 0.5354 (p90) cc_final: 0.3371 (m-80) outliers start: 35 outliers final: 23 residues processed: 188 average time/residue: 0.2080 time to fit residues: 59.3921 Evaluate side-chains 182 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 850 TRP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.0020 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12996 Z= 0.168 Angle : 0.570 10.700 17792 Z= 0.277 Chirality : 0.043 0.476 2182 Planarity : 0.004 0.035 2194 Dihedral : 5.839 81.866 2030 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.25 % Allowed : 15.72 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1742 helix: 2.16 (0.18), residues: 882 sheet: -0.57 (0.42), residues: 146 loop : -1.67 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.003 0.000 HIS A 344 PHE 0.017 0.001 PHE A 545 TYR 0.010 0.001 TYR B 292 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.5072 (tt) REVERT: A 484 ASP cc_start: 0.7802 (t0) cc_final: 0.7504 (t0) REVERT: A 587 MET cc_start: 0.7217 (tpt) cc_final: 0.6957 (tpp) REVERT: A 1059 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.3101 (m-80) REVERT: B 251 MET cc_start: 0.4988 (mtt) cc_final: 0.4786 (mtt) REVERT: B 410 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5692 (tt) REVERT: B 484 ASP cc_start: 0.7750 (t0) cc_final: 0.7471 (t0) REVERT: B 536 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6758 (t0) REVERT: B 587 MET cc_start: 0.7085 (tpt) cc_final: 0.6745 (tpp) REVERT: B 808 TRP cc_start: 0.5572 (p-90) cc_final: 0.5257 (p-90) REVERT: B 1059 PHE cc_start: 0.5423 (p90) cc_final: 0.3398 (m-80) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.2180 time to fit residues: 59.7573 Evaluate side-chains 179 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 160 optimal weight: 0.3980 chunk 146 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12996 Z= 0.201 Angle : 0.583 10.840 17792 Z= 0.283 Chirality : 0.044 0.476 2182 Planarity : 0.004 0.036 2194 Dihedral : 5.643 73.789 2030 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.33 % Allowed : 16.14 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.61 (0.21), residues: 1742 helix: 1.98 (0.18), residues: 900 sheet: 0.38 (0.44), residues: 120 loop : -1.75 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.003 0.000 HIS A 344 PHE 0.017 0.001 PHE A 545 TYR 0.009 0.001 TYR A 292 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.5306 (tt) REVERT: A 484 ASP cc_start: 0.7717 (t0) cc_final: 0.7435 (t0) REVERT: A 587 MET cc_start: 0.7233 (tpt) cc_final: 0.6888 (tpp) REVERT: A 603 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7771 (mmm-85) REVERT: A 808 TRP cc_start: 0.5802 (p-90) cc_final: 0.5470 (p-90) REVERT: B 484 ASP cc_start: 0.7765 (t0) cc_final: 0.7475 (t0) REVERT: B 536 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6757 (t0) REVERT: B 587 MET cc_start: 0.7121 (tpt) cc_final: 0.6772 (tpp) REVERT: B 808 TRP cc_start: 0.5600 (p-90) cc_final: 0.5288 (p-90) outliers start: 28 outliers final: 22 residues processed: 175 average time/residue: 0.2097 time to fit residues: 56.2189 Evaluate side-chains 175 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12996 Z= 0.163 Angle : 0.565 10.446 17792 Z= 0.272 Chirality : 0.042 0.461 2182 Planarity : 0.004 0.036 2194 Dihedral : 5.272 60.312 2030 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 16.39 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.70 (0.21), residues: 1742 helix: 2.12 (0.18), residues: 900 sheet: -0.45 (0.43), residues: 146 loop : -1.64 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.018 0.001 PHE B1059 TYR 0.009 0.001 TYR A 292 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 ASP cc_start: 0.7681 (t0) cc_final: 0.7441 (t0) REVERT: A 587 MET cc_start: 0.7127 (tpt) cc_final: 0.6793 (tpp) REVERT: A 808 TRP cc_start: 0.5741 (p-90) cc_final: 0.5441 (p-90) REVERT: A 1078 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.4728 (ptt90) REVERT: B 484 ASP cc_start: 0.7807 (t0) cc_final: 0.7538 (t0) REVERT: B 536 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6729 (t0) REVERT: B 587 MET cc_start: 0.7041 (tpt) cc_final: 0.6727 (tpp) REVERT: B 808 TRP cc_start: 0.5561 (p-90) cc_final: 0.5232 (p-90) outliers start: 27 outliers final: 21 residues processed: 176 average time/residue: 0.2180 time to fit residues: 58.7277 Evaluate side-chains 173 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1059 PHE Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 0.0370 chunk 173 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 138 optimal weight: 0.0060 chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12996 Z= 0.204 Angle : 0.591 9.648 17792 Z= 0.284 Chirality : 0.044 0.467 2182 Planarity : 0.004 0.037 2194 Dihedral : 5.176 56.476 2030 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.91 % Allowed : 16.72 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.61 (0.21), residues: 1742 helix: 2.01 (0.18), residues: 900 sheet: -0.49 (0.43), residues: 150 loop : -1.66 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.019 0.001 PHE B1059 TYR 0.010 0.001 TYR B 292 ARG 0.006 0.000 ARG B 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 ASP cc_start: 0.7702 (t0) cc_final: 0.7451 (t0) REVERT: A 587 MET cc_start: 0.7163 (tpt) cc_final: 0.6867 (tpp) REVERT: A 808 TRP cc_start: 0.5786 (p-90) cc_final: 0.5498 (p-90) REVERT: A 1078 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.4747 (ptt90) REVERT: B 484 ASP cc_start: 0.7736 (t0) cc_final: 0.7465 (t0) REVERT: B 536 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6744 (t0) REVERT: B 587 MET cc_start: 0.7110 (tpt) cc_final: 0.6767 (tpp) REVERT: B 808 TRP cc_start: 0.5610 (p-90) cc_final: 0.5292 (p-90) outliers start: 23 outliers final: 19 residues processed: 169 average time/residue: 0.2075 time to fit residues: 54.7348 Evaluate side-chains 172 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1059 PHE Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 138 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.186814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159121 restraints weight = 16668.311| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.46 r_work: 0.3857 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 0.134 12996 Z= 0.230 Angle : 0.822 59.199 17792 Z= 0.459 Chirality : 0.047 0.838 2182 Planarity : 0.004 0.051 2194 Dihedral : 5.194 56.285 2030 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.66 % Allowed : 17.14 % Favored : 81.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.60 (0.21), residues: 1742 helix: 2.00 (0.18), residues: 900 sheet: -0.49 (0.43), residues: 150 loop : -1.66 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.018 0.001 PHE B1059 TYR 0.010 0.001 TYR B 292 ARG 0.005 0.000 ARG B 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.89 seconds wall clock time: 48 minutes 23.96 seconds (2903.96 seconds total)