Starting phenix.real_space_refine on Fri May 16 18:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu4_45927/05_2025/9cu4_45927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu4_45927/05_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_45927/05_2025/9cu4_45927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu4_45927/05_2025/9cu4_45927.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu4_45927/05_2025/9cu4_45927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu4_45927/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 11.43, per 1000 atoms: 0.78 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: 4.08 Conformation dependent library (CDL) restraints added in 2.0 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: 1.97 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: 5.03 Time building geometry restraints manager: 4.68 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: 0.10 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: 5.690 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.560 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- 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 : 1.699 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: 0.2938 time to fit residues: 60.8065 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 : 1.791 ------------------------------------------------------------------------------- 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 = 0.104456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074604 restraints weight = 29987.591| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.99 r_work: 0.2991 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 1.475 Fit side-chains REVERT: A 82 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 215 ARG cc_start: 0.6903 (ttt180) cc_final: 0.6018 (tpm170) REVERT: A 233 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8728 (tp30) REVERT: B 404 MET cc_start: 0.8840 (mmt) cc_final: 0.8371 (mmt) REVERT: C 215 ARG cc_start: 0.6946 (ttt180) cc_final: 0.6056 (tpt170) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 0.2707 time to fit residues: 31.4683 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 : 1.549 ------------------------------------------------------------------------------- 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: 2.9990 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 = 0.3570 r_free = 0.3570 target = 0.103106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072313 restraints weight = 30785.887| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.97 r_work: 0.2954 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15078 Z= 0.173 Angle : 0.633 8.092 20634 Z= 0.330 Chirality : 0.048 0.343 2502 Planarity : 0.005 0.069 2532 Dihedral : 8.936 75.033 3030 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.38 % Allowed : 7.77 % Favored : 91.86 % 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: -0.57 (0.19), residues: 1743 helix: -0.17 (0.29), residues: 300 sheet: 0.58 (0.21), residues: 540 loop : -1.03 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 305 HIS 0.004 0.001 HIS B 336 PHE 0.018 0.001 PHE B 238 TYR 0.025 0.001 TYR A 92 ARG 0.008 0.000 ARG B 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 27) link_NAG-ASN : angle 1.76692 ( 81) link_ALPHA1-6 : bond 0.00281 ( 6) link_ALPHA1-6 : angle 2.23483 ( 18) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 1.23351 ( 27) link_ALPHA1-2 : bond 0.00768 ( 3) link_ALPHA1-2 : angle 3.86600 ( 9) link_ALPHA1-3 : bond 0.01205 ( 6) link_ALPHA1-3 : angle 1.62648 ( 18) hydrogen bonds : bond 0.05482 ( 542) hydrogen bonds : angle 4.69182 ( 1761) SS BOND : bond 0.00264 ( 15) SS BOND : angle 0.83502 ( 30) covalent geometry : bond 0.00406 (15012) covalent geometry : angle 0.61268 (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 69 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.608 Fit side-chains REVERT: A 82 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 233 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8771 (tp30) REVERT: C 215 ARG cc_start: 0.6871 (ttt180) cc_final: 0.5921 (tpt170) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.2568 time to fit residues: 27.7804 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 : 1.666 ------------------------------------------------------------------------------- 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: 0.3980 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 221 ASN B 455 ASN C 221 ASN C 455 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068782 restraints weight = 30306.624| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.01 r_work: 0.2862 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15078 Z= 0.249 Angle : 0.666 8.010 20634 Z= 0.347 Chirality : 0.050 0.348 2502 Planarity : 0.006 0.048 2532 Dihedral : 8.773 72.983 3030 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.39 % Allowed : 8.78 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1743 helix: -0.50 (0.28), residues: 321 sheet: 0.46 (0.22), residues: 513 loop : -1.20 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 305 HIS 0.006 0.002 HIS B 669 PHE 0.022 0.002 PHE B 238 TYR 0.017 0.002 TYR A 92 ARG 0.007 0.001 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 27) link_NAG-ASN : angle 1.85061 ( 81) link_ALPHA1-6 : bond 0.00211 ( 6) link_ALPHA1-6 : angle 2.33366 ( 18) link_BETA1-4 : bond 0.00360 ( 9) link_BETA1-4 : angle 1.53903 ( 27) link_ALPHA1-2 : bond 0.00677 ( 3) link_ALPHA1-2 : angle 3.80994 ( 9) link_ALPHA1-3 : bond 0.01040 ( 6) link_ALPHA1-3 : angle 1.68532 ( 18) hydrogen bonds : bond 0.06024 ( 542) hydrogen bonds : angle 4.67457 ( 1761) SS BOND : bond 0.00305 ( 15) SS BOND : angle 0.96491 ( 30) covalent geometry : bond 0.00606 (15012) covalent geometry : angle 0.64483 (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 89 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.645 Fit side-chains REVERT: B 233 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8818 (tm-30) outliers start: 22 outliers final: 8 residues processed: 88 average time/residue: 0.2384 time to fit residues: 33.4710 Evaluate side-chains 70 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 0.0040 chunk 150 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071470 restraints weight = 30854.100| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.15 r_work: 0.2911 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15078 Z= 0.117 Angle : 0.561 8.175 20634 Z= 0.288 Chirality : 0.046 0.353 2502 Planarity : 0.004 0.050 2532 Dihedral : 7.927 65.090 3030 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.88 % Allowed : 9.22 % Favored : 89.90 % 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: 0.22 (0.30), residues: 306 sheet: 0.70 (0.22), residues: 513 loop : -1.10 (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 0.012 0.001 PHE A 238 TYR 0.018 0.001 TYR C 301 ARG 0.008 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 27) link_NAG-ASN : angle 1.43932 ( 81) link_ALPHA1-6 : bond 0.00487 ( 6) link_ALPHA1-6 : angle 2.21261 ( 18) link_BETA1-4 : bond 0.00440 ( 9) link_BETA1-4 : angle 1.36313 ( 27) link_ALPHA1-2 : bond 0.00803 ( 3) link_ALPHA1-2 : angle 4.08316 ( 9) link_ALPHA1-3 : bond 0.01159 ( 6) link_ALPHA1-3 : angle 1.38041 ( 18) hydrogen bonds : bond 0.04647 ( 542) hydrogen bonds : angle 4.32808 ( 1761) SS BOND : bond 0.00246 ( 15) SS BOND : angle 0.69249 ( 30) covalent geometry : bond 0.00249 (15012) covalent geometry : angle 0.54088 (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 80 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.351 Fit side-chains REVERT: B 649 ARG cc_start: 0.8684 (tmm-80) cc_final: 0.8458 (tmm-80) outliers start: 14 outliers final: 4 residues processed: 79 average time/residue: 0.2432 time to fit residues: 30.8866 Evaluate side-chains 60 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 145 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072134 restraints weight = 30092.963| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.04 r_work: 0.2926 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15078 Z= 0.115 Angle : 0.561 8.213 20634 Z= 0.287 Chirality : 0.046 0.350 2502 Planarity : 0.004 0.045 2532 Dihedral : 7.613 62.109 3030 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.51 % Allowed : 9.91 % Favored : 89.58 % 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: -0.32 (0.19), residues: 1743 helix: 0.46 (0.30), residues: 306 sheet: 0.78 (0.23), residues: 513 loop : -1.03 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.002 0.001 HIS C 336 PHE 0.011 0.001 PHE B 238 TYR 0.016 0.001 TYR A 92 ARG 0.008 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 27) link_NAG-ASN : angle 1.35115 ( 81) link_ALPHA1-6 : bond 0.00544 ( 6) link_ALPHA1-6 : angle 2.19662 ( 18) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.34721 ( 27) link_ALPHA1-2 : bond 0.00810 ( 3) link_ALPHA1-2 : angle 3.98304 ( 9) link_ALPHA1-3 : bond 0.01115 ( 6) link_ALPHA1-3 : angle 1.43192 ( 18) hydrogen bonds : bond 0.04427 ( 542) hydrogen bonds : angle 4.19444 ( 1761) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.66572 ( 30) covalent geometry : bond 0.00247 (15012) covalent geometry : angle 0.54274 (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: 8 poor density : 61 time to evaluate : 1.614 Fit side-chains REVERT: B 649 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8486 (tmm-80) REVERT: C 506 MET cc_start: 0.8436 (mmt) cc_final: 0.8198 (mmt) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.2368 time to fit residues: 25.9374 Evaluate side-chains 62 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 616 THR Chi-restraints excluded: chain C residue 67 VAL 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: 2.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 30 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.101699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071867 restraints weight = 30268.118| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.04 r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15078 Z= 0.126 Angle : 0.561 8.189 20634 Z= 0.287 Chirality : 0.046 0.350 2502 Planarity : 0.004 0.047 2532 Dihedral : 7.435 59.342 3030 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.57 % Allowed : 10.42 % Favored : 89.02 % 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: 0.60 (0.30), residues: 306 sheet: 0.86 (0.23), residues: 513 loop : -1.00 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.001 PHE B 238 TYR 0.016 0.001 TYR B 92 ARG 0.009 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 27) link_NAG-ASN : angle 1.32648 ( 81) link_ALPHA1-6 : bond 0.00569 ( 6) link_ALPHA1-6 : angle 2.24151 ( 18) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 1.36952 ( 27) link_ALPHA1-2 : bond 0.00796 ( 3) link_ALPHA1-2 : angle 3.94708 ( 9) link_ALPHA1-3 : bond 0.01047 ( 6) link_ALPHA1-3 : angle 1.41102 ( 18) hydrogen bonds : bond 0.04516 ( 542) hydrogen bonds : angle 4.17121 ( 1761) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.67671 ( 30) covalent geometry : bond 0.00285 (15012) covalent geometry : angle 0.54267 (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 71 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.757 Fit side-chains REVERT: A 215 ARG cc_start: 0.6792 (ttt180) cc_final: 0.5801 (tpm170) REVERT: B 649 ARG cc_start: 0.8717 (tmm-80) cc_final: 0.8500 (tmm-80) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.2798 time to fit residues: 30.5114 Evaluate side-chains 65 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.102021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071582 restraints weight = 30770.960| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.16 r_work: 0.2920 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15078 Z= 0.127 Angle : 0.557 8.149 20634 Z= 0.283 Chirality : 0.046 0.350 2502 Planarity : 0.004 0.041 2532 Dihedral : 7.306 56.990 3030 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.51 % Allowed : 10.54 % 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: -0.19 (0.20), residues: 1743 helix: 0.62 (0.30), residues: 306 sheet: 0.90 (0.23), residues: 513 loop : -1.00 (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 0.013 0.001 PHE C 238 TYR 0.016 0.001 TYR C 92 ARG 0.006 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 27) link_NAG-ASN : angle 1.31645 ( 81) link_ALPHA1-6 : bond 0.00604 ( 6) link_ALPHA1-6 : angle 2.27521 ( 18) link_BETA1-4 : bond 0.00420 ( 9) link_BETA1-4 : angle 1.40043 ( 27) link_ALPHA1-2 : bond 0.00799 ( 3) link_ALPHA1-2 : angle 3.94765 ( 9) link_ALPHA1-3 : bond 0.01024 ( 6) link_ALPHA1-3 : angle 1.39142 ( 18) hydrogen bonds : bond 0.04474 ( 542) hydrogen bonds : angle 4.15723 ( 1761) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.67020 ( 30) covalent geometry : bond 0.00288 (15012) covalent geometry : angle 0.53878 (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 70 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.509 Fit side-chains REVERT: A 215 ARG cc_start: 0.6658 (ttt180) cc_final: 0.5704 (tpm170) REVERT: A 649 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8543 (tmm-80) REVERT: B 215 ARG cc_start: 0.6659 (ttt180) cc_final: 0.5675 (tpm170) REVERT: B 649 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8543 (tmm-80) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.2668 time to fit residues: 28.4344 Evaluate side-chains 67 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070043 restraints weight = 30179.171| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.01 r_work: 0.2884 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15078 Z= 0.194 Angle : 0.618 9.572 20634 Z= 0.315 Chirality : 0.047 0.350 2502 Planarity : 0.005 0.046 2532 Dihedral : 7.635 59.870 3030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.69 % Allowed : 11.11 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1743 helix: 0.13 (0.29), residues: 324 sheet: 0.80 (0.23), residues: 513 loop : -1.06 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS C 108 PHE 0.019 0.001 PHE C 238 TYR 0.017 0.001 TYR C 92 ARG 0.007 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 27) link_NAG-ASN : angle 1.50011 ( 81) link_ALPHA1-6 : bond 0.00452 ( 6) link_ALPHA1-6 : angle 2.36901 ( 18) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 1.59175 ( 27) link_ALPHA1-2 : bond 0.00775 ( 3) link_ALPHA1-2 : angle 3.82086 ( 9) link_ALPHA1-3 : bond 0.00897 ( 6) link_ALPHA1-3 : angle 1.47951 ( 18) hydrogen bonds : bond 0.05226 ( 542) hydrogen bonds : angle 4.33282 ( 1761) SS BOND : bond 0.00263 ( 15) SS BOND : angle 0.76813 ( 30) covalent geometry : bond 0.00472 (15012) covalent geometry : angle 0.59914 (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 74 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.575 Fit side-chains REVERT: B 649 ARG cc_start: 0.8793 (tmm-80) cc_final: 0.8592 (tmm-80) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2420 time to fit residues: 27.8724 Evaluate side-chains 71 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 178 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.0030 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.100610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.070826 restraints weight = 30257.995| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.04 r_work: 0.2902 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15078 Z= 0.148 Angle : 0.582 7.951 20634 Z= 0.297 Chirality : 0.046 0.352 2502 Planarity : 0.004 0.045 2532 Dihedral : 6.790 53.591 3030 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -0.37 (0.20), residues: 1743 helix: 0.21 (0.29), residues: 324 sheet: 0.86 (0.23), residues: 513 loop : -1.08 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 305 HIS 0.002 0.001 HIS B 108 PHE 0.014 0.001 PHE B 238 TYR 0.016 0.001 TYR C 92 ARG 0.008 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 27) link_NAG-ASN : angle 1.41929 ( 81) link_ALPHA1-6 : bond 0.00378 ( 6) link_ALPHA1-6 : angle 2.27973 ( 18) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 1.59069 ( 27) link_ALPHA1-2 : bond 0.00793 ( 3) link_ALPHA1-2 : angle 3.92473 ( 9) link_ALPHA1-3 : bond 0.00846 ( 6) link_ALPHA1-3 : angle 1.55626 ( 18) hydrogen bonds : bond 0.04838 ( 542) hydrogen bonds : angle 4.27605 ( 1761) SS BOND : bond 0.00248 ( 15) SS BOND : angle 0.71602 ( 30) covalent geometry : bond 0.00351 (15012) covalent geometry : angle 0.56205 (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 73 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.537 Fit side-chains REVERT: A 215 ARG cc_start: 0.6865 (ttt180) cc_final: 0.5837 (tpm170) REVERT: B 215 ARG cc_start: 0.6713 (ttt180) cc_final: 0.5665 (tpm170) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.2698 time to fit residues: 30.1898 Evaluate side-chains 72 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 178 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 616 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 616 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070746 restraints weight = 30416.181| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.05 r_work: 0.2902 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15078 Z= 0.148 Angle : 0.577 7.856 20634 Z= 0.296 Chirality : 0.046 0.352 2502 Planarity : 0.004 0.046 2532 Dihedral : 6.442 52.317 3030 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -0.34 (0.20), residues: 1743 helix: 0.20 (0.29), residues: 324 sheet: 0.82 (0.23), residues: 528 loop : -1.05 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS C 108 PHE 0.016 0.001 PHE C 238 TYR 0.018 0.001 TYR C 92 ARG 0.009 0.000 ARG C 649 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 27) link_NAG-ASN : angle 1.41454 ( 81) link_ALPHA1-6 : bond 0.00306 ( 6) link_ALPHA1-6 : angle 2.23653 ( 18) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 1.57715 ( 27) link_ALPHA1-2 : bond 0.00789 ( 3) link_ALPHA1-2 : angle 3.87737 ( 9) link_ALPHA1-3 : bond 0.00879 ( 6) link_ALPHA1-3 : angle 1.39131 ( 18) hydrogen bonds : bond 0.04818 ( 542) hydrogen bonds : angle 4.26312 ( 1761) SS BOND : bond 0.00248 ( 15) SS BOND : angle 0.70236 ( 30) covalent geometry : bond 0.00351 (15012) covalent geometry : angle 0.55779 (20451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5575.85 seconds wall clock time: 98 minutes 19.60 seconds (5899.60 seconds total)