Starting phenix.real_space_refine on Fri Jun 13 05:52:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu4_45927/06_2025/9cu4_45927.cif" } resolution = 3.3 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= 0.012 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9264 2.51 5 N 2385 2.21 5 O 2979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4662 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 25, 'TRANS': 559} Chain breaks: 1 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Restraints were copied for chains: G, I, F, H, C, B Time building chain proxies: 11.65, per 1000 atoms: 0.79 Number of scatterers: 14688 At special positions: 0 Unit cell: (97.18, 96.32, 193.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2979 8.00 N 2385 7.00 C 9264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 587 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN D 5 " - " MAN D 6 " " MAN F 5 " - " MAN F 6 " " MAN H 5 " - " MAN H 6 " ALPHA1-3 " BMA D 3 " - " MAN D 8 " " MAN D 4 " - " MAN D 7 " " BMA F 3 " - " MAN F 8 " " MAN F 4 " - " MAN F 7 " " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 701 " - " ASN A 628 " " NAG A 702 " - " ASN A 275 " " NAG A 703 " - " ASN A 355 " " NAG A 704 " - " ASN A 368 " " NAG A 705 " - " ASN A 372 " " NAG A 706 " - " ASN A 385 " " NAG A 707 " - " ASN A 599 " " NAG B 701 " - " ASN B 628 " " NAG B 702 " - " ASN B 275 " " NAG B 703 " - " ASN B 355 " " NAG B 704 " - " ASN B 368 " " NAG B 705 " - " ASN B 372 " " NAG B 706 " - " ASN B 385 " " NAG B 707 " - " ASN B 599 " " NAG C 701 " - " ASN C 628 " " NAG C 702 " - " ASN C 275 " " NAG C 703 " - " ASN C 355 " " NAG C 704 " - " ASN C 368 " " NAG C 705 " - " ASN C 372 " " NAG C 706 " - " ASN C 385 " " NAG C 707 " - " ASN C 599 " " NAG D 1 " - " ASN A 179 " " NAG E 1 " - " ASN A 254 " " NAG F 1 " - " ASN B 179 " " NAG G 1 " - " ASN B 254 " " NAG H 1 " - " ASN C 179 " " NAG I 1 " - " ASN C 254 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.9 seconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 20.5% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 144 through 154 removed outlier: 4.581A pdb=" N HIS A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 365 through 379 removed outlier: 4.101A pdb=" N THR A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 499 removed outlier: 3.730A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Proline residue: A 470 - end of helix removed outlier: 3.766A pdb=" N VAL A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.100A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 656 through 670 removed outlier: 4.517A pdb=" N ARG A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 removed outlier: 4.581A pdb=" N HIS B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 365 through 379 removed outlier: 4.101A pdb=" N THR B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 499 removed outlier: 3.730A pdb=" N GLN B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Proline residue: B 470 - end of helix removed outlier: 3.765A pdb=" N VAL B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 486 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 499 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 4.100A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 644 through 651 Processing helix chain 'B' and resid 656 through 670 removed outlier: 4.517A pdb=" N ARG B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 154 removed outlier: 4.582A pdb=" N HIS C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 365 through 379 removed outlier: 4.101A pdb=" N THR C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 499 removed outlier: 3.730A pdb=" N GLN C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Proline residue: C 470 - end of helix removed outlier: 3.766A pdb=" N VAL C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 486 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 510 removed outlier: 4.100A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 644 through 651 Processing helix chain 'C' and resid 656 through 670 removed outlier: 4.517A pdb=" N ARG C 662 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 530 removed outlier: 6.749A pdb=" N ARG A 66 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 515 through 518 removed outlier: 3.557A pdb=" N GLU A 75 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 76 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 621 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG A 78 " --> pdb=" O LEU B 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE A 327 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 319 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS A 102 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 321 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 325 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 96 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 327 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 94 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 95 " --> pdb=" O MET A 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE A 327 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 319 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS A 102 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 321 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 325 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 96 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 327 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 94 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 95 " --> pdb=" O MET A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 6.306A pdb=" N ILE A 133 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 125 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 135 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 187 removed outlier: 4.803A pdb=" N ARG A 196 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LYS A 111 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA A 306 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 301 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLN A 291 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 269 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA8, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 551 removed outlier: 4.418A pdb=" N CYS A 550 " --> pdb=" O VAL A 584 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 592 through 596 removed outlier: 3.589A pdb=" N ARG A 611 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS A 605 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 619 through 621 removed outlier: 3.806A pdb=" N SER A 619 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 75 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 529 through 530 removed outlier: 6.749A pdb=" N ARG B 66 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 515 through 518 removed outlier: 3.557A pdb=" N GLU B 75 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 76 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU C 621 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG B 78 " --> pdb=" O LEU C 621 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE B 327 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 319 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS B 102 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 321 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG B 325 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 96 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 327 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN B 94 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 95 " --> pdb=" O MET B 404 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE B 327 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 319 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS B 102 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 321 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG B 325 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 96 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 327 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN B 94 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 95 " --> pdb=" O MET B 404 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 141 removed outlier: 6.306A pdb=" N ILE B 133 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B 125 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 135 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 removed outlier: 4.803A pdb=" N ARG B 196 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LYS B 111 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA B 306 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 301 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLN B 291 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 269 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AC1, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 removed outlier: 4.417A pdb=" N CYS B 550 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 592 through 596 removed outlier: 3.590A pdb=" N ARG B 611 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 605 " --> pdb=" O TYR B 609 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 529 through 530 removed outlier: 6.749A pdb=" N ARG C 66 " --> pdb=" O ILE C 577 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE C 327 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU C 319 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS C 102 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 321 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG C 325 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 96 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 327 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN C 94 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU C 95 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 344 through 349 removed outlier: 4.101A pdb=" N ILE C 327 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU C 319 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS C 102 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 321 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG C 325 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 96 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 327 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN C 94 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU C 95 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 132 through 141 removed outlier: 6.306A pdb=" N ILE C 133 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 125 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C 135 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 185 through 187 removed outlier: 4.804A pdb=" N ARG C 196 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LYS C 111 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA C 306 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLN C 291 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 269 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 156 through 157 Processing sheet with id=AD1, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AD2, first strand: chain 'C' and resid 550 through 551 removed outlier: 4.417A pdb=" N CYS C 550 " --> pdb=" O VAL C 584 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 592 through 596 removed outlier: 3.590A pdb=" N ARG C 611 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS C 605 " --> pdb=" O TYR C 609 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1761 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: 5.24 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4090 1.34 - 1.46: 2777 1.46 - 1.58: 8064 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 15012 Sorted by residual: bond pdb=" C5 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 15007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13894 1.80 - 3.60: 5528 3.60 - 5.40: 957 5.40 - 7.19: 66 7.19 - 8.99: 6 Bond angle restraints: 20451 Sorted by residual: angle pdb=" CA ASP B 532 " pdb=" CB ASP B 532 " pdb=" CG ASP B 532 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA ASP C 532 " pdb=" CB ASP C 532 " pdb=" CG ASP C 532 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA ASP A 532 " pdb=" CB ASP A 532 " pdb=" CG ASP A 532 " ideal model delta sigma weight residual 112.60 118.65 -6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" CA PHE A 198 " pdb=" CB PHE A 198 " pdb=" CG PHE A 198 " ideal model delta sigma weight residual 113.80 119.66 -5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" CA PHE C 198 " pdb=" CB PHE C 198 " pdb=" CG PHE C 198 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.42e+01 ... (remaining 20446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 9171 21.51 - 43.01: 366 43.01 - 64.52: 78 64.52 - 86.02: 27 86.02 - 107.53: 12 Dihedral angle restraints: 9654 sinusoidal: 4449 harmonic: 5205 Sorted by residual: dihedral pdb=" CA GLY B 208 " pdb=" C GLY B 208 " pdb=" N TRP B 209 " pdb=" CA TRP B 209 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 208 " pdb=" C GLY A 208 " pdb=" N TRP A 209 " pdb=" CA TRP A 209 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY C 208 " pdb=" C GLY C 208 " pdb=" N TRP C 209 " pdb=" CA TRP C 209 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 9651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 2338 0.172 - 0.344: 146 0.344 - 0.516: 12 0.516 - 0.688: 3 0.688 - 0.860: 3 Chirality restraints: 2502 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.12e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.12e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.10e+02 ... (remaining 2499 not shown) Planarity restraints: 2559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 704 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG C 704 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C 704 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG C 704 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG C 704 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG A 704 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 704 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG B 704 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B 704 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG B 704 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG B 704 " 0.188 2.00e-02 2.50e+03 ... (remaining 2556 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 12 2.23 - 2.90: 5187 2.90 - 3.56: 17563 3.56 - 4.23: 30651 4.23 - 4.90: 51676 Nonbonded interactions: 105089 Sorted by model distance: nonbonded pdb=" OE2 GLU B 130 " pdb=" OG1 THR C 171 " model vdw 1.559 3.040 nonbonded pdb=" OE2 GLU A 130 " pdb=" OG1 THR B 171 " model vdw 1.559 3.040 nonbonded pdb=" OG1 THR A 171 " pdb=" OE2 GLU C 130 " model vdw 1.559 3.040 nonbonded pdb=" OE1 GLN B 83 " pdb=" CZ PHE C 624 " model vdw 2.122 3.340 nonbonded pdb=" OE1 GLN A 83 " pdb=" CZ PHE B 624 " model vdw 2.122 3.340 ... (remaining 105084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 7.540 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.060 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.013 0.071 15078 Z= 0.807 Angle : 1.848 8.992 20634 Z= 1.216 Chirality : 0.101 0.860 2502 Planarity : 0.027 0.305 2532 Dihedral : 13.501 107.531 6249 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.76 % Allowed : 0.95 % Favored : 98.30 % Cbeta Deviations : 0.18 % 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: -1.06 (0.19), residues: 1743 helix: -2.14 (0.24), residues: 321 sheet: 0.84 (0.23), residues: 477 loop : -0.98 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.017 TRP B 320 HIS 0.010 0.004 HIS A 669 PHE 0.054 0.010 PHE C 238 TYR 0.098 0.016 TYR C 101 ARG 0.007 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 27) link_NAG-ASN : angle 3.72471 ( 81) link_ALPHA1-6 : bond 0.01008 ( 6) link_ALPHA1-6 : angle 2.36435 ( 18) link_BETA1-4 : bond 0.00870 ( 9) link_BETA1-4 : angle 2.56837 ( 27) link_ALPHA1-2 : bond 0.01313 ( 3) link_ALPHA1-2 : angle 4.82992 ( 9) link_ALPHA1-3 : bond 0.01080 ( 6) link_ALPHA1-3 : angle 2.84766 ( 18) hydrogen bonds : bond 0.19561 ( 542) hydrogen bonds : angle 7.30722 ( 1761) SS BOND : bond 0.00884 ( 15) SS BOND : angle 1.73587 ( 30) covalent geometry : bond 0.01318 (15012) covalent geometry : angle 1.83209 (20451) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.7700 (ttt180) cc_final: 0.7185 (tpt170) REVERT: B 215 ARG cc_start: 0.7727 (ttt180) cc_final: 0.7217 (tpm170) REVERT: C 215 ARG cc_start: 0.7655 (ttt180) cc_final: 0.7217 (tpt170) REVERT: C 404 MET cc_start: 0.8819 (mmm) cc_final: 0.8450 (mmt) outliers start: 12 outliers final: 3 residues processed: 144 average time/residue: 0.3039 time to fit residues: 63.3078 Evaluate side-chains 85 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain C residue 149 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074615 restraints weight = 29993.578| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.99 r_work: 0.2992 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15078 Z= 0.166 Angle : 0.741 9.054 20634 Z= 0.384 Chirality : 0.051 0.340 2502 Planarity : 0.005 0.039 2532 Dihedral : 9.781 77.240 3033 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.44 % 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: -0.53 (0.19), residues: 1743 helix: -0.63 (0.29), residues: 300 sheet: 0.67 (0.21), residues: 549 loop : -0.89 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 305 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 210 TYR 0.014 0.001 TYR A 301 ARG 0.005 0.001 ARG C 675 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 2.58973 ( 81) link_ALPHA1-6 : bond 0.00103 ( 6) link_ALPHA1-6 : angle 2.22294 ( 18) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.65238 ( 27) link_ALPHA1-2 : bond 0.00591 ( 3) link_ALPHA1-2 : angle 3.91389 ( 9) link_ALPHA1-3 : bond 0.00882 ( 6) link_ALPHA1-3 : angle 1.88307 ( 18) hydrogen bonds : bond 0.05803 ( 542) hydrogen bonds : angle 5.22580 ( 1761) SS BOND : bond 0.00279 ( 15) SS BOND : angle 1.09974 ( 30) covalent geometry : bond 0.00342 (15012) covalent geometry : angle 0.71255 (20451) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 1.706 Fit side-chains REVERT: A 82 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 215 ARG cc_start: 0.6903 (ttt180) cc_final: 0.6018 (tpm170) REVERT: A 233 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8728 (tp30) REVERT: B 404 MET cc_start: 0.8839 (mmt) cc_final: 0.8371 (mmt) REVERT: C 215 ARG cc_start: 0.6945 (ttt180) cc_final: 0.6056 (tpt170) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 0.2710 time to fit residues: 31.6474 Evaluate side-chains 59 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072252 restraints weight = 30778.638| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.02 r_work: 0.2953 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15078 Z= 0.173 Angle : 0.636 8.029 20634 Z= 0.331 Chirality : 0.048 0.343 2502 Planarity : 0.005 0.068 2532 Dihedral : 9.009 75.219 3030 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.38 % Allowed : 7.70 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1743 helix: -0.19 (0.29), residues: 300 sheet: 0.55 (0.21), residues: 546 loop : -1.01 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 305 HIS 0.003 0.001 HIS B 336 PHE 0.016 0.001 PHE B 238 TYR 0.024 0.001 TYR A 92 ARG 0.007 0.000 ARG B 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 27) link_NAG-ASN : angle 1.82793 ( 81) link_ALPHA1-6 : bond 0.00256 ( 6) link_ALPHA1-6 : angle 2.23660 ( 18) link_BETA1-4 : bond 0.00354 ( 9) link_BETA1-4 : angle 1.26368 ( 27) link_ALPHA1-2 : bond 0.00746 ( 3) link_ALPHA1-2 : angle 3.87724 ( 9) link_ALPHA1-3 : bond 0.01252 ( 6) link_ALPHA1-3 : angle 1.70667 ( 18) hydrogen bonds : bond 0.05519 ( 542) hydrogen bonds : angle 4.72519 ( 1761) SS BOND : bond 0.00267 ( 15) SS BOND : angle 0.84108 ( 30) covalent geometry : bond 0.00403 (15012) covalent geometry : angle 0.61546 (20451) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.692 Fit side-chains REVERT: A 82 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 233 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8776 (tp30) REVERT: C 215 ARG cc_start: 0.6918 (ttt180) cc_final: 0.5958 (tpt170) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.2623 time to fit residues: 28.6514 Evaluate side-chains 60 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070763 restraints weight = 30074.810| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.01 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15078 Z= 0.175 Angle : 0.603 8.129 20634 Z= 0.312 Chirality : 0.048 0.348 2502 Planarity : 0.005 0.041 2532 Dihedral : 8.320 70.182 3030 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.14 % Allowed : 8.40 % Favored : 90.47 % 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: -0.61 (0.19), residues: 1743 helix: -0.03 (0.29), residues: 306 sheet: 0.60 (0.22), residues: 513 loop : -1.13 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 305 HIS 0.004 0.001 HIS A 93 PHE 0.016 0.001 PHE C 238 TYR 0.012 0.001 TYR B 92 ARG 0.008 0.000 ARG B 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 27) link_NAG-ASN : angle 1.60059 ( 81) link_ALPHA1-6 : bond 0.00340 ( 6) link_ALPHA1-6 : angle 2.24784 ( 18) link_BETA1-4 : bond 0.00395 ( 9) link_BETA1-4 : angle 1.34279 ( 27) link_ALPHA1-2 : bond 0.00733 ( 3) link_ALPHA1-2 : angle 3.90709 ( 9) link_ALPHA1-3 : bond 0.01090 ( 6) link_ALPHA1-3 : angle 1.56264 ( 18) hydrogen bonds : bond 0.05219 ( 542) hydrogen bonds : angle 4.47426 ( 1761) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.78488 ( 30) covalent geometry : bond 0.00416 (15012) covalent geometry : angle 0.58276 (20451) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.722 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 0.2348 time to fit residues: 31.1454 Evaluate side-chains 66 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 586 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.070990 restraints weight = 30152.056| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.01 r_work: 0.2905 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15078 Z= 0.155 Angle : 0.579 8.136 20634 Z= 0.298 Chirality : 0.047 0.349 2502 Planarity : 0.005 0.047 2532 Dihedral : 8.018 66.797 3030 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 8.90 % Favored : 90.09 % 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: -0.48 (0.19), residues: 1743 helix: 0.18 (0.30), residues: 306 sheet: 0.69 (0.23), residues: 507 loop : -1.08 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 305 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.001 PHE C 238 TYR 0.018 0.001 TYR C 301 ARG 0.009 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 27) link_NAG-ASN : angle 1.48558 ( 81) link_ALPHA1-6 : bond 0.00413 ( 6) link_ALPHA1-6 : angle 2.24361 ( 18) link_BETA1-4 : bond 0.00413 ( 9) link_BETA1-4 : angle 1.35808 ( 27) link_ALPHA1-2 : bond 0.00752 ( 3) link_ALPHA1-2 : angle 3.94145 ( 9) link_ALPHA1-3 : bond 0.01093 ( 6) link_ALPHA1-3 : angle 1.50871 ( 18) hydrogen bonds : bond 0.05064 ( 542) hydrogen bonds : angle 4.36400 ( 1761) SS BOND : bond 0.00254 ( 15) SS BOND : angle 0.73068 ( 30) covalent geometry : bond 0.00362 (15012) covalent geometry : angle 0.55916 (20451) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.670 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 80 average time/residue: 0.2363 time to fit residues: 30.4508 Evaluate side-chains 65 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070786 restraints weight = 31029.678| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.18 r_work: 0.2900 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15078 Z= 0.146 Angle : 0.580 8.166 20634 Z= 0.298 Chirality : 0.047 0.350 2502 Planarity : 0.004 0.046 2532 Dihedral : 7.823 64.235 3030 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.57 % Allowed : 9.34 % Favored : 90.09 % 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: -0.39 (0.19), residues: 1743 helix: 0.31 (0.30), residues: 306 sheet: 0.73 (0.23), residues: 513 loop : -1.04 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE B 238 TYR 0.014 0.001 TYR C 301 ARG 0.009 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 27) link_NAG-ASN : angle 1.44159 ( 81) link_ALPHA1-6 : bond 0.00465 ( 6) link_ALPHA1-6 : angle 2.23573 ( 18) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 1.37091 ( 27) link_ALPHA1-2 : bond 0.00774 ( 3) link_ALPHA1-2 : angle 3.94504 ( 9) link_ALPHA1-3 : bond 0.01069 ( 6) link_ALPHA1-3 : angle 1.47179 ( 18) hydrogen bonds : bond 0.04871 ( 542) hydrogen bonds : angle 4.29640 ( 1761) SS BOND : bond 0.00249 ( 15) SS BOND : angle 0.72027 ( 30) covalent geometry : bond 0.00338 (15012) covalent geometry : angle 0.56149 (20451) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.708 Fit side-chains REVERT: A 210 PHE cc_start: 0.8424 (t80) cc_final: 0.8143 (t80) outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.2471 time to fit residues: 26.7200 Evaluate side-chains 65 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 30 optimal weight: 0.0030 chunk 17 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072888 restraints weight = 30189.295| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.05 r_work: 0.2941 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15078 Z= 0.110 Angle : 0.551 8.227 20634 Z= 0.280 Chirality : 0.046 0.352 2502 Planarity : 0.004 0.047 2532 Dihedral : 7.322 58.777 3030 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.82 % Allowed : 9.72 % Favored : 89.46 % 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: -0.21 (0.20), residues: 1743 helix: 0.59 (0.30), residues: 306 sheet: 0.85 (0.23), residues: 513 loop : -0.98 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.002 0.001 HIS B 336 PHE 0.010 0.001 PHE C 238 TYR 0.016 0.001 TYR C 92 ARG 0.010 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 27) link_NAG-ASN : angle 1.28342 ( 81) link_ALPHA1-6 : bond 0.00623 ( 6) link_ALPHA1-6 : angle 2.18628 ( 18) link_BETA1-4 : bond 0.00456 ( 9) link_BETA1-4 : angle 1.31727 ( 27) link_ALPHA1-2 : bond 0.00805 ( 3) link_ALPHA1-2 : angle 4.03979 ( 9) link_ALPHA1-3 : bond 0.01058 ( 6) link_ALPHA1-3 : angle 1.31028 ( 18) hydrogen bonds : bond 0.04244 ( 542) hydrogen bonds : angle 4.14548 ( 1761) SS BOND : bond 0.00242 ( 15) SS BOND : angle 0.64815 ( 30) covalent geometry : bond 0.00234 (15012) covalent geometry : angle 0.53242 (20451) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.699 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.2361 time to fit residues: 30.7243 Evaluate side-chains 70 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069213 restraints weight = 31150.262| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.16 r_work: 0.2870 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15078 Z= 0.233 Angle : 0.637 8.224 20634 Z= 0.328 Chirality : 0.048 0.350 2502 Planarity : 0.005 0.048 2532 Dihedral : 7.873 62.511 3030 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.69 % Allowed : 10.35 % Favored : 88.95 % 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: -0.47 (0.19), residues: 1743 helix: 0.01 (0.29), residues: 324 sheet: 0.74 (0.23), residues: 513 loop : -1.06 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 305 HIS 0.004 0.001 HIS B 108 PHE 0.020 0.001 PHE C 238 TYR 0.022 0.002 TYR B 92 ARG 0.006 0.001 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 27) link_NAG-ASN : angle 1.58400 ( 81) link_ALPHA1-6 : bond 0.00448 ( 6) link_ALPHA1-6 : angle 2.35874 ( 18) link_BETA1-4 : bond 0.00344 ( 9) link_BETA1-4 : angle 1.53983 ( 27) link_ALPHA1-2 : bond 0.00739 ( 3) link_ALPHA1-2 : angle 3.78495 ( 9) link_ALPHA1-3 : bond 0.00876 ( 6) link_ALPHA1-3 : angle 1.55133 ( 18) hydrogen bonds : bond 0.05527 ( 542) hydrogen bonds : angle 4.40127 ( 1761) SS BOND : bond 0.00272 ( 15) SS BOND : angle 0.81407 ( 30) covalent geometry : bond 0.00572 (15012) covalent geometry : angle 0.61818 (20451) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.765 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.2455 time to fit residues: 27.6385 Evaluate side-chains 70 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 28 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071580 restraints weight = 29947.268| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.02 r_work: 0.2916 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15078 Z= 0.128 Angle : 0.579 8.177 20634 Z= 0.295 Chirality : 0.046 0.354 2502 Planarity : 0.004 0.043 2532 Dihedral : 7.482 57.592 3030 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.69 % Allowed : 10.61 % Favored : 88.70 % 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: -0.28 (0.20), residues: 1743 helix: 0.50 (0.30), residues: 306 sheet: 0.86 (0.23), residues: 513 loop : -1.06 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.002 0.001 HIS B 108 PHE 0.013 0.001 PHE C 238 TYR 0.018 0.001 TYR C 92 ARG 0.007 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 27) link_NAG-ASN : angle 1.37965 ( 81) link_ALPHA1-6 : bond 0.00583 ( 6) link_ALPHA1-6 : angle 2.26914 ( 18) link_BETA1-4 : bond 0.00461 ( 9) link_BETA1-4 : angle 1.42956 ( 27) link_ALPHA1-2 : bond 0.00802 ( 3) link_ALPHA1-2 : angle 4.01227 ( 9) link_ALPHA1-3 : bond 0.01035 ( 6) link_ALPHA1-3 : angle 1.37290 ( 18) hydrogen bonds : bond 0.04637 ( 542) hydrogen bonds : angle 4.27362 ( 1761) SS BOND : bond 0.00235 ( 15) SS BOND : angle 0.68764 ( 30) covalent geometry : bond 0.00289 (15012) covalent geometry : angle 0.56018 (20451) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.742 Fit side-chains REVERT: A 215 ARG cc_start: 0.6836 (ttt180) cc_final: 0.5810 (tpm170) REVERT: A 649 ARG cc_start: 0.8830 (tmm-80) cc_final: 0.8538 (tmm-80) REVERT: B 215 ARG cc_start: 0.6852 (ttt180) cc_final: 0.5795 (tpm170) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.3152 time to fit residues: 36.6648 Evaluate side-chains 73 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069755 restraints weight = 30438.980| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.02 r_work: 0.2881 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15078 Z= 0.204 Angle : 0.634 10.968 20634 Z= 0.323 Chirality : 0.047 0.351 2502 Planarity : 0.005 0.049 2532 Dihedral : 7.619 58.882 3030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.51 % Allowed : 11.36 % Favored : 88.13 % 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: -0.51 (0.19), residues: 1743 helix: 0.00 (0.29), residues: 324 sheet: 0.76 (0.23), residues: 513 loop : -1.14 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.004 0.001 HIS B 108 PHE 0.019 0.001 PHE A 238 TYR 0.019 0.001 TYR C 92 ARG 0.007 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 27) link_NAG-ASN : angle 1.55039 ( 81) link_ALPHA1-6 : bond 0.00396 ( 6) link_ALPHA1-6 : angle 2.29962 ( 18) link_BETA1-4 : bond 0.00411 ( 9) link_BETA1-4 : angle 1.65182 ( 27) link_ALPHA1-2 : bond 0.00768 ( 3) link_ALPHA1-2 : angle 3.81631 ( 9) link_ALPHA1-3 : bond 0.00902 ( 6) link_ALPHA1-3 : angle 1.49352 ( 18) hydrogen bonds : bond 0.05358 ( 542) hydrogen bonds : angle 4.38680 ( 1761) SS BOND : bond 0.00264 ( 15) SS BOND : angle 0.78974 ( 30) covalent geometry : bond 0.00497 (15012) covalent geometry : angle 0.61492 (20451) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.592 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.2359 time to fit residues: 26.6002 Evaluate side-chains 71 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 0.0170 chunk 72 optimal weight: 0.0060 chunk 25 optimal weight: 0.0010 chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072119 restraints weight = 30927.134| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.18 r_work: 0.2930 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15078 Z= 0.109 Angle : 0.567 9.577 20634 Z= 0.287 Chirality : 0.045 0.354 2502 Planarity : 0.004 0.043 2532 Dihedral : 6.446 52.276 3030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.57 % Allowed : 11.36 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1743 helix: 0.63 (0.31), residues: 306 sheet: 0.96 (0.23), residues: 507 loop : -1.11 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 305 HIS 0.002 0.000 HIS A 593 PHE 0.010 0.001 PHE B 238 TYR 0.018 0.001 TYR C 92 ARG 0.007 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 27) link_NAG-ASN : angle 1.28298 ( 81) link_ALPHA1-6 : bond 0.00474 ( 6) link_ALPHA1-6 : angle 2.25684 ( 18) link_BETA1-4 : bond 0.00466 ( 9) link_BETA1-4 : angle 1.49717 ( 27) link_ALPHA1-2 : bond 0.00828 ( 3) link_ALPHA1-2 : angle 4.04170 ( 9) link_ALPHA1-3 : bond 0.00956 ( 6) link_ALPHA1-3 : angle 1.42110 ( 18) hydrogen bonds : bond 0.04246 ( 542) hydrogen bonds : angle 4.17624 ( 1761) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.66847 ( 30) covalent geometry : bond 0.00234 (15012) covalent geometry : angle 0.54844 (20451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6251.50 seconds wall clock time: 110 minutes 36.30 seconds (6636.30 seconds total)