Starting phenix.real_space_refine on Thu Sep 18 06:34:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu4_45927/09_2025/9cu4_45927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu4_45927/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cu4_45927/09_2025/9cu4_45927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu4_45927/09_2025/9cu4_45927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cu4_45927/09_2025/9cu4_45927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu4_45927/09_2025/9cu4_45927.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, F, H, G, I Time building chain proxies: 4.54, per 1000 atoms: 0.31 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 B 68 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 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: 1.52 Conformation dependent library (CDL) restraints added in 618.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 2.93 Time building geometry restraints manager: 1.95 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 6.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 284 TYR 0.098 0.016 TYR C 101 PHE 0.054 0.010 PHE C 238 TRP 0.051 0.017 TRP B 320 HIS 0.010 0.004 HIS A 669 Details of bonding type rmsd covalent geometry : bond 0.01318 (15012) covalent geometry : angle 1.83209 (20451) SS BOND : bond 0.00884 ( 15) SS BOND : angle 1.73587 ( 30) hydrogen bonds : bond 0.19561 ( 542) hydrogen bonds : angle 7.30722 ( 1761) 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) 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_NAG-ASN : bond 0.00751 ( 27) link_NAG-ASN : angle 3.72471 ( 81) *********************** 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 : 0.578 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: 0.1513 time to fit residues: 31.2418 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 : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074430 restraints weight = 30124.995| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.00 r_work: 0.2986 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15078 Z= 0.172 Angle : 0.738 8.636 20634 Z= 0.382 Chirality : 0.050 0.341 2502 Planarity : 0.005 0.037 2532 Dihedral : 9.789 76.937 3033 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.19), residues: 1743 helix: -0.86 (0.28), residues: 318 sheet: 0.68 (0.21), residues: 549 loop : -0.88 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 675 TYR 0.013 0.002 TYR A 604 PHE 0.013 0.002 PHE A 210 TRP 0.016 0.002 TRP A 305 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00353 (15012) covalent geometry : angle 0.70962 (20451) SS BOND : bond 0.00277 ( 15) SS BOND : angle 1.07052 ( 30) hydrogen bonds : bond 0.05859 ( 542) hydrogen bonds : angle 5.18936 ( 1761) link_ALPHA1-2 : bond 0.01030 ( 3) link_ALPHA1-2 : angle 3.70799 ( 9) link_ALPHA1-3 : bond 0.01097 ( 6) link_ALPHA1-3 : angle 1.91765 ( 18) link_ALPHA1-6 : bond 0.00275 ( 6) link_ALPHA1-6 : angle 2.33840 ( 18) link_BETA1-4 : bond 0.00237 ( 9) link_BETA1-4 : angle 1.61262 ( 27) link_NAG-ASN : bond 0.00302 ( 27) link_NAG-ASN : angle 2.58334 ( 81) *********************** 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 76 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.552 Fit side-chains REVERT: A 82 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 215 ARG cc_start: 0.6901 (ttt180) cc_final: 0.6006 (tpm170) REVERT: A 233 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8724 (tp30) REVERT: B 404 MET cc_start: 0.8834 (mmt) cc_final: 0.8405 (mmt) REVERT: C 215 ARG cc_start: 0.6943 (ttt180) cc_final: 0.6046 (tpt170) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.1192 time to fit residues: 13.5540 Evaluate side-chains 57 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 144 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.103943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074209 restraints weight = 30496.386| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.02 r_work: 0.2985 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15078 Z= 0.130 Angle : 0.593 8.091 20634 Z= 0.308 Chirality : 0.047 0.344 2502 Planarity : 0.004 0.038 2532 Dihedral : 8.592 72.728 3030 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.19), residues: 1743 helix: -0.04 (0.30), residues: 303 sheet: 0.70 (0.22), residues: 528 loop : -0.93 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 649 TYR 0.026 0.001 TYR B 92 PHE 0.014 0.001 PHE B 238 TRP 0.013 0.001 TRP A 305 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00274 (15012) covalent geometry : angle 0.57372 (20451) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.74222 ( 30) hydrogen bonds : bond 0.04907 ( 542) hydrogen bonds : angle 4.54992 ( 1761) link_ALPHA1-2 : bond 0.00868 ( 3) link_ALPHA1-2 : angle 3.94923 ( 9) link_ALPHA1-3 : bond 0.01215 ( 6) link_ALPHA1-3 : angle 1.53822 ( 18) link_ALPHA1-6 : bond 0.00389 ( 6) link_ALPHA1-6 : angle 2.18565 ( 18) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.22758 ( 27) link_NAG-ASN : bond 0.00292 ( 27) link_NAG-ASN : angle 1.59483 ( 81) *********************** 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 71 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.604 Fit side-chains REVERT: A 80 ASN cc_start: 0.8957 (t0) cc_final: 0.8717 (t0) REVERT: A 82 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 233 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8787 (tp30) REVERT: B 404 MET cc_start: 0.8842 (mmt) cc_final: 0.8348 (mmt) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.1136 time to fit residues: 12.7167 Evaluate side-chains 59 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 167 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 455 ASN C 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.069779 restraints weight = 30484.814| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.02 r_work: 0.2883 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15078 Z= 0.235 Angle : 0.652 8.055 20634 Z= 0.340 Chirality : 0.049 0.346 2502 Planarity : 0.005 0.046 2532 Dihedral : 8.589 72.561 3030 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.20 % Allowed : 8.46 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 1743 helix: -0.41 (0.28), residues: 324 sheet: 0.54 (0.22), residues: 513 loop : -1.13 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 649 TYR 0.016 0.002 TYR A 92 PHE 0.020 0.002 PHE B 238 TRP 0.016 0.002 TRP A 305 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00572 (15012) covalent geometry : angle 0.63190 (20451) SS BOND : bond 0.00311 ( 15) SS BOND : angle 0.91277 ( 30) hydrogen bonds : bond 0.05774 ( 542) hydrogen bonds : angle 4.60407 ( 1761) link_ALPHA1-2 : bond 0.00712 ( 3) link_ALPHA1-2 : angle 3.78695 ( 9) link_ALPHA1-3 : bond 0.00979 ( 6) link_ALPHA1-3 : angle 1.64467 ( 18) link_ALPHA1-6 : bond 0.00263 ( 6) link_ALPHA1-6 : angle 2.31515 ( 18) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 1.40054 ( 27) link_NAG-ASN : bond 0.00272 ( 27) link_NAG-ASN : angle 1.73459 ( 81) *********************** 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 81 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.591 Fit side-chains REVERT: A 210 PHE cc_start: 0.8597 (t80) cc_final: 0.8391 (t80) REVERT: B 649 ARG cc_start: 0.8754 (tmm-80) cc_final: 0.8512 (tmm-80) outliers start: 19 outliers final: 7 residues processed: 80 average time/residue: 0.1131 time to fit residues: 14.5406 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 : 0.519 ------------------------------------------------------------------------------- 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 125 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072063 restraints weight = 30040.536| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.03 r_work: 0.2923 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2979 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= 0.119 Angle : 0.561 8.185 20634 Z= 0.289 Chirality : 0.046 0.350 2502 Planarity : 0.004 0.047 2532 Dihedral : 7.949 66.447 3030 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.88 % Allowed : 8.90 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1743 helix: 0.31 (0.30), residues: 303 sheet: 0.73 (0.23), residues: 507 loop : -1.02 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 649 TYR 0.018 0.001 TYR C 301 PHE 0.012 0.001 PHE A 238 TRP 0.012 0.001 TRP C 305 HIS 0.002 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00253 (15012) covalent geometry : angle 0.54170 (20451) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.69327 ( 30) hydrogen bonds : bond 0.04667 ( 542) hydrogen bonds : angle 4.33446 ( 1761) link_ALPHA1-2 : bond 0.00784 ( 3) link_ALPHA1-2 : angle 4.04664 ( 9) link_ALPHA1-3 : bond 0.01136 ( 6) link_ALPHA1-3 : angle 1.43322 ( 18) link_ALPHA1-6 : bond 0.00481 ( 6) link_ALPHA1-6 : angle 2.20393 ( 18) link_BETA1-4 : bond 0.00449 ( 9) link_BETA1-4 : angle 1.32606 ( 27) link_NAG-ASN : bond 0.00258 ( 27) link_NAG-ASN : angle 1.43725 ( 81) *********************** 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 77 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.585 Fit side-chains REVERT: A 210 PHE cc_start: 0.8451 (t80) cc_final: 0.8206 (t80) REVERT: B 649 ARG cc_start: 0.8769 (tmm-80) cc_final: 0.8529 (tmm-80) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.1191 time to fit residues: 14.1266 Evaluate side-chains 61 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.0070 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.100881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070279 restraints weight = 30998.344| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.14 r_work: 0.2894 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15078 Z= 0.174 Angle : 0.599 8.142 20634 Z= 0.309 Chirality : 0.047 0.348 2502 Planarity : 0.005 0.047 2532 Dihedral : 7.953 65.748 3030 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.38 % Allowed : 9.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 1743 helix: 0.27 (0.30), residues: 306 sheet: 0.70 (0.22), residues: 513 loop : -1.02 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 649 TYR 0.015 0.001 TYR C 301 PHE 0.016 0.001 PHE C 238 TRP 0.012 0.001 TRP A 305 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00415 (15012) covalent geometry : angle 0.57977 (20451) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.77807 ( 30) hydrogen bonds : bond 0.05135 ( 542) hydrogen bonds : angle 4.33796 ( 1761) link_ALPHA1-2 : bond 0.00776 ( 3) link_ALPHA1-2 : angle 3.83610 ( 9) link_ALPHA1-3 : bond 0.01007 ( 6) link_ALPHA1-3 : angle 1.54026 ( 18) link_ALPHA1-6 : bond 0.00389 ( 6) link_ALPHA1-6 : angle 2.25943 ( 18) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.40090 ( 27) link_NAG-ASN : bond 0.00245 ( 27) link_NAG-ASN : angle 1.50412 ( 81) *********************** 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 66 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.635 Fit side-chains REVERT: A 210 PHE cc_start: 0.8434 (t80) cc_final: 0.8163 (t80) REVERT: B 649 ARG cc_start: 0.8766 (tmm-80) cc_final: 0.8526 (tmm-80) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1232 time to fit residues: 12.5765 Evaluate side-chains 63 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 B residue 148 ILE Chi-restraints excluded: chain C residue 67 VAL 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 130 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 141 optimal weight: 0.0170 chunk 112 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.102669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072927 restraints weight = 29850.041| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.03 r_work: 0.2940 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15078 Z= 0.109 Angle : 0.555 8.213 20634 Z= 0.283 Chirality : 0.046 0.353 2502 Planarity : 0.004 0.046 2532 Dihedral : 7.405 59.777 3030 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.82 % Allowed : 10.04 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.19), residues: 1743 helix: 0.59 (0.30), residues: 306 sheet: 0.90 (0.23), residues: 507 loop : -1.01 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 649 TYR 0.016 0.001 TYR A 92 PHE 0.011 0.001 PHE A 238 TRP 0.011 0.001 TRP A 305 HIS 0.002 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00228 (15012) covalent geometry : angle 0.53669 (20451) SS BOND : bond 0.00236 ( 15) SS BOND : angle 0.65263 ( 30) hydrogen bonds : bond 0.04253 ( 542) hydrogen bonds : angle 4.18145 ( 1761) link_ALPHA1-2 : bond 0.00804 ( 3) link_ALPHA1-2 : angle 4.08380 ( 9) link_ALPHA1-3 : bond 0.01121 ( 6) link_ALPHA1-3 : angle 1.33846 ( 18) link_ALPHA1-6 : bond 0.00609 ( 6) link_ALPHA1-6 : angle 2.18645 ( 18) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.32073 ( 27) link_NAG-ASN : bond 0.00265 ( 27) link_NAG-ASN : angle 1.30717 ( 81) *********************** 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 83 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.515 Fit side-chains REVERT: A 215 ARG cc_start: 0.6829 (ttt180) cc_final: 0.5815 (tpm170) REVERT: B 215 ARG cc_start: 0.6772 (ttt180) cc_final: 0.5789 (tpm170) REVERT: B 649 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8570 (tmm-80) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1188 time to fit residues: 14.9371 Evaluate side-chains 68 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.102643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072126 restraints weight = 30807.335| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.19 r_work: 0.2926 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15078 Z= 0.124 Angle : 0.564 8.214 20634 Z= 0.287 Chirality : 0.046 0.348 2502 Planarity : 0.004 0.040 2532 Dihedral : 7.332 58.881 3030 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.57 % Allowed : 10.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 1743 helix: 0.63 (0.30), residues: 306 sheet: 0.87 (0.23), residues: 513 loop : -1.02 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 649 TYR 0.019 0.001 TYR A 92 PHE 0.013 0.001 PHE C 238 TRP 0.010 0.001 TRP A 305 HIS 0.002 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00279 (15012) covalent geometry : angle 0.54620 (20451) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.65229 ( 30) hydrogen bonds : bond 0.04420 ( 542) hydrogen bonds : angle 4.15413 ( 1761) link_ALPHA1-2 : bond 0.00813 ( 3) link_ALPHA1-2 : angle 3.91598 ( 9) link_ALPHA1-3 : bond 0.01020 ( 6) link_ALPHA1-3 : angle 1.41900 ( 18) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 2.21346 ( 18) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 1.34673 ( 27) link_NAG-ASN : bond 0.00229 ( 27) link_NAG-ASN : angle 1.31712 ( 81) *********************** 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: 9 poor density : 61 time to evaluate : 0.601 Fit side-chains REVERT: A 215 ARG cc_start: 0.6815 (ttt180) cc_final: 0.5816 (tpm170) REVERT: A 649 ARG cc_start: 0.8858 (tmm-80) cc_final: 0.8561 (tmm-80) REVERT: B 215 ARG cc_start: 0.6776 (ttt180) cc_final: 0.5767 (tpm170) REVERT: B 649 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8589 (tmm-80) outliers start: 9 outliers final: 9 residues processed: 69 average time/residue: 0.1240 time to fit residues: 13.1714 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 : 0.707 ------------------------------------------------------------------------------- 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 178 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 55 optimal weight: 1.9990 chunk 112 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.103193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.072788 restraints weight = 30937.816| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.16 r_work: 0.2938 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15078 Z= 0.115 Angle : 0.562 8.219 20634 Z= 0.285 Chirality : 0.046 0.351 2502 Planarity : 0.004 0.039 2532 Dihedral : 7.130 56.360 3030 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.57 % Allowed : 10.67 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1743 helix: 0.72 (0.30), residues: 306 sheet: 0.99 (0.23), residues: 507 loop : -1.03 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 649 TYR 0.018 0.001 TYR A 92 PHE 0.013 0.001 PHE C 238 TRP 0.011 0.001 TRP A 305 HIS 0.002 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00253 (15012) covalent geometry : angle 0.54480 (20451) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.63778 ( 30) hydrogen bonds : bond 0.04219 ( 542) hydrogen bonds : angle 4.11756 ( 1761) link_ALPHA1-2 : bond 0.00806 ( 3) link_ALPHA1-2 : angle 3.99605 ( 9) link_ALPHA1-3 : bond 0.01042 ( 6) link_ALPHA1-3 : angle 1.34946 ( 18) link_ALPHA1-6 : bond 0.00670 ( 6) link_ALPHA1-6 : angle 2.21942 ( 18) link_BETA1-4 : bond 0.00451 ( 9) link_BETA1-4 : angle 1.33109 ( 27) link_NAG-ASN : bond 0.00240 ( 27) link_NAG-ASN : angle 1.26544 ( 81) *********************** 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: 9 poor density : 65 time to evaluate : 0.579 Fit side-chains REVERT: A 215 ARG cc_start: 0.6659 (ttt180) cc_final: 0.5731 (tpm170) REVERT: A 649 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8531 (tmm-80) REVERT: B 215 ARG cc_start: 0.6592 (ttt180) cc_final: 0.5657 (tpm170) REVERT: B 649 ARG cc_start: 0.8800 (tmm-80) cc_final: 0.8581 (tmm-80) REVERT: C 215 ARG cc_start: 0.6665 (ttt180) cc_final: 0.5690 (tpm170) outliers start: 9 outliers final: 9 residues processed: 72 average time/residue: 0.1431 time to fit residues: 15.3880 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 : 0.579 ------------------------------------------------------------------------------- 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 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 139 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.102014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072348 restraints weight = 29938.298| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.02 r_work: 0.2932 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15078 Z= 0.132 Angle : 0.575 8.991 20634 Z= 0.290 Chirality : 0.046 0.350 2502 Planarity : 0.004 0.039 2532 Dihedral : 7.164 56.240 3030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.63 % Allowed : 10.98 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1743 helix: 0.65 (0.30), residues: 306 sheet: 0.96 (0.23), residues: 507 loop : -1.08 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 649 TYR 0.018 0.001 TYR A 92 PHE 0.013 0.001 PHE B 238 TRP 0.010 0.001 TRP A 305 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00305 (15012) covalent geometry : angle 0.55703 (20451) SS BOND : bond 0.00224 ( 15) SS BOND : angle 0.64658 ( 30) hydrogen bonds : bond 0.04439 ( 542) hydrogen bonds : angle 4.13054 ( 1761) link_ALPHA1-2 : bond 0.00800 ( 3) link_ALPHA1-2 : angle 3.91323 ( 9) link_ALPHA1-3 : bond 0.00980 ( 6) link_ALPHA1-3 : angle 1.39342 ( 18) link_ALPHA1-6 : bond 0.00636 ( 6) link_ALPHA1-6 : angle 2.25078 ( 18) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.37495 ( 27) link_NAG-ASN : bond 0.00224 ( 27) link_NAG-ASN : angle 1.31653 ( 81) ********************** 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 75 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.705 Fit side-chains REVERT: A 215 ARG cc_start: 0.6771 (ttt180) cc_final: 0.5810 (tpm170) REVERT: B 215 ARG cc_start: 0.6790 (ttt180) cc_final: 0.5784 (tpm170) REVERT: B 649 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8598 (tmm-80) REVERT: C 215 ARG cc_start: 0.6826 (ttt180) cc_final: 0.5786 (tpm170) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1352 time to fit residues: 14.8239 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 : 0.574 ------------------------------------------------------------------------------- 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 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 165 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.070531 restraints weight = 30816.359| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.17 r_work: 0.2899 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15078 Z= 0.164 Angle : 0.595 9.823 20634 Z= 0.303 Chirality : 0.047 0.351 2502 Planarity : 0.004 0.044 2532 Dihedral : 7.403 57.037 3030 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.69 % Allowed : 10.92 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.20), residues: 1743 helix: 0.21 (0.29), residues: 324 sheet: 0.93 (0.23), residues: 507 loop : -1.10 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 649 TYR 0.018 0.001 TYR A 92 PHE 0.015 0.001 PHE B 238 TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00392 (15012) covalent geometry : angle 0.57611 (20451) SS BOND : bond 0.00246 ( 15) SS BOND : angle 0.70491 ( 30) hydrogen bonds : bond 0.04913 ( 542) hydrogen bonds : angle 4.25342 ( 1761) link_ALPHA1-2 : bond 0.00784 ( 3) link_ALPHA1-2 : angle 3.87491 ( 9) link_ALPHA1-3 : bond 0.00940 ( 6) link_ALPHA1-3 : angle 1.44474 ( 18) link_ALPHA1-6 : bond 0.00566 ( 6) link_ALPHA1-6 : angle 2.29292 ( 18) link_BETA1-4 : bond 0.00440 ( 9) link_BETA1-4 : angle 1.49685 ( 27) link_NAG-ASN : bond 0.00220 ( 27) link_NAG-ASN : angle 1.44462 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.66 seconds wall clock time: 52 minutes 44.04 seconds (3164.04 seconds total)