Starting phenix.real_space_refine on Thu Sep 18 05:15:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jli_61589/09_2025/9jli_61589.map" } resolution = 2.84 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= 0.008 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 57 5.16 5 C 8934 2.51 5 N 2334 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 14104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4678 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'TYR:plan': 4, 'ARG:plan': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'TYR:plan': 5, 'ARG:plan': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "C" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'TYR:plan': 5, 'ARG:plan': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "A" 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: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.40, per 1000 atoms: 0.24 Number of scatterers: 14104 At special positions: 0 Unit cell: (94.38, 93.06, 182.82, 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 57 16.00 O 2779 8.00 N 2334 7.00 C 8934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 482 " distance=2.04 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 482 " distance=2.04 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 482 " distance=2.04 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 438 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 548 " distance=2.03 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 Atom "HETATM14032 O5 NAG A 701 .*. O " rejected from bonding due to valence issues. Atom "HETATM14060 O5 NAG B 701 .*. O " rejected from bonding due to valence issues. Atom "HETATM14088 O5 NAG C 701 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 329 " " NAG B 702 " - " ASN B 329 " " NAG C 702 " - " ASN C 329 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 684.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 22.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.815A pdb=" N ASN A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 410 through 453 removed outlier: 3.954A pdb=" N GLN A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.569A pdb=" N ILE A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 616 through 631 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.814A pdb=" N ASN B 259 " --> pdb=" O ASN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 410 through 453 removed outlier: 3.954A pdb=" N GLN B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.569A pdb=" N ILE B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 616 through 631 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 164 through 167 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.814A pdb=" N ASN C 259 " --> pdb=" O ASN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 353 Processing helix chain 'C' and resid 410 through 453 removed outlier: 3.954A pdb=" N GLN C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 453 " --> pdb=" O HIS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 465 removed outlier: 3.569A pdb=" N ILE C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 579 Processing helix chain 'C' and resid 605 through 612 Processing helix chain 'C' and resid 616 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.886A pdb=" N LEU A 515 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG A 39 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 477 through 478 removed outlier: 7.458A pdb=" N LEU C 582 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG A 51 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.541A pdb=" N SER A 359 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS A 368 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A 324 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 74 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 297 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE A 72 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 299 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 70 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 301 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 68 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 303 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 66 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU A 69 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 162 removed outlier: 4.829A pdb=" N GLU A 281 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 262 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 251 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 264 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A 266 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 138 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 499 removed outlier: 4.609A pdb=" N VAL A 498 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 553 through 558 removed outlier: 3.630A pdb=" N SER A 558 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 572 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR A 566 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AB2, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.886A pdb=" N LEU B 515 " --> pdb=" O TYR B 493 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG B 39 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.541A pdb=" N SER B 359 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS B 368 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 324 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE B 74 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR B 297 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE B 72 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR B 299 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY B 70 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 301 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 68 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 303 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS B 66 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 69 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 162 removed outlier: 4.828A pdb=" N GLU B 281 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 262 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 251 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 264 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 249 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG B 266 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'B' and resid 134 through 138 Processing sheet with id=AB8, first strand: chain 'B' and resid 497 through 499 removed outlier: 4.609A pdb=" N VAL B 498 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 553 through 558 removed outlier: 3.631A pdb=" N SER B 558 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 572 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR B 566 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N HIS B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 29 removed outlier: 4.886A pdb=" N LEU C 515 " --> pdb=" O TYR C 493 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 39 " --> pdb=" O ILE C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.541A pdb=" N SER C 359 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS C 368 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER C 324 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE C 74 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR C 297 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE C 72 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR C 299 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 70 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 301 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER C 68 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG C 303 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS C 66 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU C 69 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 162 removed outlier: 4.828A pdb=" N GLU C 281 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 262 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 251 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 264 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 249 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG C 266 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AC7, first strand: chain 'C' and resid 134 through 138 Processing sheet with id=AC8, first strand: chain 'C' and resid 497 through 499 removed outlier: 4.608A pdb=" N VAL C 498 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 553 through 558 removed outlier: 3.630A pdb=" N SER C 558 " --> pdb=" O HIS C 561 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 572 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR C 566 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N HIS C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1536 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: 2.55 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4517 1.34 - 1.46: 3307 1.46 - 1.59: 6479 1.59 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 14387 Sorted by residual: bond pdb=" N CYS C 58 " pdb=" CA CYS C 58 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.63e+00 bond pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.73e+00 bond pdb=" N VAL A 402 " pdb=" CA VAL A 402 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.66e+00 bond pdb=" N VAL C 402 " pdb=" CA VAL C 402 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.46e+00 bond pdb=" N CYS A 58 " pdb=" CA CYS A 58 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.04e+00 ... (remaining 14382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 19289 2.00 - 3.99: 231 3.99 - 5.99: 39 5.99 - 7.98: 3 7.98 - 9.98: 3 Bond angle restraints: 19565 Sorted by residual: angle pdb=" CB MET C 351 " pdb=" CG MET C 351 " pdb=" SD MET C 351 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB MET A 351 " pdb=" CG MET A 351 " pdb=" SD MET A 351 " ideal model delta sigma weight residual 112.70 122.67 -9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB MET B 351 " pdb=" CG MET B 351 " pdb=" SD MET B 351 " ideal model delta sigma weight residual 112.70 122.65 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA CYS C 58 " pdb=" C CYS C 58 " pdb=" O CYS C 58 " ideal model delta sigma weight residual 121.66 117.93 3.73 1.22e+00 6.72e-01 9.33e+00 angle pdb=" CA PRO C 60 " pdb=" C PRO C 60 " pdb=" O PRO C 60 " ideal model delta sigma weight residual 121.23 118.22 3.01 1.07e+00 8.73e-01 7.94e+00 ... (remaining 19560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 7457 15.48 - 30.96: 934 30.96 - 46.44: 267 46.44 - 61.92: 84 61.92 - 77.40: 27 Dihedral angle restraints: 8769 sinusoidal: 3419 harmonic: 5350 Sorted by residual: dihedral pdb=" CA CYS A 41 " pdb=" CB CYS A 41 " pdb=" SG CYS A 41 " pdb=" SG CYS A 482 " ideal model delta sinusoidal sigma weight residual 79.00 8.97 70.03 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA CYS C 41 " pdb=" CB CYS C 41 " pdb=" SG CYS C 41 " pdb=" SG CYS C 482 " ideal model delta sinusoidal sigma weight residual 79.00 8.98 70.02 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA CYS B 41 " pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 482 " ideal model delta sinusoidal sigma weight residual 79.00 9.00 70.00 1 2.00e+01 2.50e-03 1.58e+01 ... (remaining 8766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.080: 2280 1.080 - 2.161: 0 2.161 - 3.241: 0 3.241 - 4.322: 0 4.322 - 5.402: 3 Chirality restraints: 2283 Sorted by residual: chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 329 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 3.00 -5.40 2.00e-01 2.50e+01 7.30e+02 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 329 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 3.00 -5.40 2.00e-01 2.50e+01 7.29e+02 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 3.00 -5.40 2.00e-01 2.50e+01 7.29e+02 ... (remaining 2280 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.010 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN A 329 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.127 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 329 " -0.010 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN B 329 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 329 " -0.127 2.00e-02 2.50e+03 pdb=" ND2 ASN B 329 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 329 " -0.009 2.00e-02 2.50e+03 1.45e-01 2.64e+02 pdb=" CG ASN C 329 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 329 " -0.127 2.00e-02 2.50e+03 pdb=" ND2 ASN C 329 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " -0.152 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 99 2.47 - 3.08: 9757 3.08 - 3.69: 20922 3.69 - 4.29: 29850 4.29 - 4.90: 50038 Nonbonded interactions: 110666 Sorted by model distance: nonbonded pdb=" ND2 ASN A 247 " pdb=" O5 NAG A 701 " model vdw 1.868 3.120 nonbonded pdb=" ND2 ASN B 247 " pdb=" O5 NAG B 701 " model vdw 1.869 3.120 nonbonded pdb=" ND2 ASN C 247 " pdb=" O5 NAG C 701 " model vdw 1.869 3.120 nonbonded pdb=" ND2 ASN C 247 " pdb=" C1 NAG C 701 " model vdw 2.093 3.550 nonbonded pdb=" ND2 ASN A 247 " pdb=" C1 NAG A 701 " model vdw 2.093 3.550 ... (remaining 110661 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 631 or (resid 632 and (name N or name CA or nam \ e C or name O or name CB )) or resid 633 through 702)) selection = chain 'B' selection = chain 'C' } 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: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.005 0.280 14402 Z= 0.256 Angle : 0.605 22.751 19598 Z= 0.287 Chirality : 0.201 5.402 2283 Planarity : 0.002 0.025 2503 Dihedral : 15.951 77.399 5271 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 28.16 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.20), residues: 1794 helix: 2.14 (0.29), residues: 348 sheet: 0.07 (0.24), residues: 435 loop : -0.75 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 87 TYR 0.021 0.001 TYR C 32 PHE 0.022 0.001 PHE A 342 TRP 0.006 0.001 TRP C 295 HIS 0.003 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00299 (14387) covalent geometry : angle 0.52767 (19565) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.37005 ( 24) hydrogen bonds : bond 0.17821 ( 533) hydrogen bonds : angle 7.63945 ( 1536) link_NAG-ASN : bond 0.27964 ( 3) link_NAG-ASN : angle 13.64429 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.509 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4352 time to fit residues: 42.6557 Evaluate side-chains 80 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 394 ASN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.048798 restraints weight = 37961.122| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 4.06 r_work: 0.2524 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14402 Z= 0.112 Angle : 0.685 24.384 19598 Z= 0.309 Chirality : 0.059 1.119 2283 Planarity : 0.003 0.025 2503 Dihedral : 5.525 43.524 2080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.17 % Allowed : 22.80 % Favored : 74.03 % 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: 0.08 (0.19), residues: 1794 helix: 2.26 (0.29), residues: 348 sheet: 0.28 (0.24), residues: 426 loop : -0.85 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.016 0.001 TYR B 61 PHE 0.019 0.001 PHE C 342 TRP 0.006 0.001 TRP B 377 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00236 (14387) covalent geometry : angle 0.56769 (19565) SS BOND : bond 0.00626 ( 12) SS BOND : angle 1.47132 ( 24) hydrogen bonds : bond 0.04062 ( 533) hydrogen bonds : angle 5.36693 ( 1536) link_NAG-ASN : bond 0.01175 ( 3) link_NAG-ASN : angle 17.79389 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.405 Fit side-chains REVERT: A 92 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: A 611 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8216 (mpp80) REVERT: B 59 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8813 (p) REVERT: B 92 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: B 266 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8271 (tpt90) REVERT: B 611 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8274 (mpp80) REVERT: C 32 TYR cc_start: 0.8358 (t80) cc_final: 0.8139 (t80) REVERT: C 92 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: C 611 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8296 (mpp80) outliers start: 48 outliers final: 10 residues processed: 121 average time/residue: 0.4086 time to fit residues: 56.1467 Evaluate side-chains 95 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 611 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 143 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 0.0980 chunk 171 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.086683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048729 restraints weight = 38194.999| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.04 r_work: 0.2528 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14402 Z= 0.115 Angle : 0.629 21.802 19598 Z= 0.290 Chirality : 0.049 0.709 2283 Planarity : 0.003 0.025 2503 Dihedral : 5.371 51.060 2080 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.04 % Allowed : 23.86 % Favored : 73.10 % 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: 0.10 (0.19), residues: 1794 helix: 2.61 (0.29), residues: 330 sheet: 0.14 (0.23), residues: 426 loop : -0.83 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.012 0.001 TYR B 61 PHE 0.020 0.001 PHE C 342 TRP 0.006 0.001 TRP B 377 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00253 (14387) covalent geometry : angle 0.53689 (19565) SS BOND : bond 0.00285 ( 12) SS BOND : angle 1.31169 ( 24) hydrogen bonds : bond 0.03773 ( 533) hydrogen bonds : angle 4.95841 ( 1536) link_NAG-ASN : bond 0.01969 ( 3) link_NAG-ASN : angle 15.19607 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.593 Fit side-chains REVERT: A 59 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 587 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8468 (mmp80) REVERT: A 611 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8254 (mpp80) REVERT: B 32 TYR cc_start: 0.8316 (t80) cc_final: 0.8028 (t80) REVERT: B 59 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 266 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (tpt90) REVERT: B 611 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8313 (mpp80) REVERT: C 587 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8479 (mtp85) REVERT: C 611 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8324 (mpp80) outliers start: 46 outliers final: 13 residues processed: 117 average time/residue: 0.4652 time to fit residues: 61.6159 Evaluate side-chains 98 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 464 TYR Chi-restraints excluded: chain C residue 587 ARG Chi-restraints excluded: chain C residue 611 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 65 optimal weight: 0.0050 chunk 27 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.0314 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.086554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.048684 restraints weight = 38163.659| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.07 r_work: 0.2526 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14402 Z= 0.111 Angle : 0.591 20.394 19598 Z= 0.275 Chirality : 0.047 0.632 2283 Planarity : 0.003 0.025 2503 Dihedral : 4.868 42.845 2080 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.64 % Allowed : 23.86 % Favored : 72.50 % 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: -0.03 (0.19), residues: 1794 helix: 2.32 (0.29), residues: 348 sheet: -0.00 (0.23), residues: 426 loop : -0.88 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 87 TYR 0.010 0.001 TYR A 32 PHE 0.020 0.001 PHE C 342 TRP 0.006 0.001 TRP B 377 HIS 0.002 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00245 (14387) covalent geometry : angle 0.50559 (19565) SS BOND : bond 0.00302 ( 12) SS BOND : angle 1.30782 ( 24) hydrogen bonds : bond 0.03507 ( 533) hydrogen bonds : angle 4.70936 ( 1536) link_NAG-ASN : bond 0.01954 ( 3) link_NAG-ASN : angle 14.12103 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 79 time to evaluate : 0.596 Fit side-chains REVERT: A 59 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9130 (p) REVERT: A 90 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8418 (ttmm) REVERT: A 92 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: A 611 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8276 (mpp80) REVERT: B 32 TYR cc_start: 0.8327 (t80) cc_final: 0.8098 (t80) REVERT: B 59 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 90 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8659 (ttmm) REVERT: B 92 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: B 266 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7982 (tpt90) REVERT: B 609 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8954 (mm) REVERT: B 611 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8329 (mpp80) REVERT: C 90 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8634 (ttmm) REVERT: C 92 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: C 611 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8340 (mpp80) outliers start: 55 outliers final: 19 residues processed: 124 average time/residue: 0.4240 time to fit residues: 60.3156 Evaluate side-chains 108 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 464 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 611 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.084750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.046114 restraints weight = 38215.954| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 4.08 r_work: 0.2446 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 14402 Z= 0.308 Angle : 0.669 20.082 19598 Z= 0.321 Chirality : 0.049 0.596 2283 Planarity : 0.003 0.021 2503 Dihedral : 5.101 42.264 2080 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 24.79 % Favored : 72.04 % 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: -0.28 (0.19), residues: 1794 helix: 2.14 (0.29), residues: 348 sheet: -0.32 (0.22), residues: 441 loop : -0.97 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 443 TYR 0.019 0.002 TYR A 208 PHE 0.033 0.002 PHE C 342 TRP 0.005 0.001 TRP C 280 HIS 0.006 0.001 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00710 (14387) covalent geometry : angle 0.60039 (19565) SS BOND : bond 0.00214 ( 12) SS BOND : angle 1.36048 ( 24) hydrogen bonds : bond 0.04358 ( 533) hydrogen bonds : angle 4.97724 ( 1536) link_NAG-ASN : bond 0.01594 ( 3) link_NAG-ASN : angle 13.68558 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 77 time to evaluate : 0.559 Fit side-chains REVERT: A 32 TYR cc_start: 0.8246 (t80) cc_final: 0.8022 (t80) REVERT: B 32 TYR cc_start: 0.8354 (t80) cc_final: 0.8134 (t80) REVERT: B 609 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8918 (mm) REVERT: C 32 TYR cc_start: 0.8313 (t80) cc_final: 0.8056 (t80) REVERT: C 587 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8466 (mmp80) outliers start: 48 outliers final: 18 residues processed: 113 average time/residue: 0.4005 time to fit residues: 52.1728 Evaluate side-chains 96 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ARG Chi-restraints excluded: chain C residue 627 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.085726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047618 restraints weight = 37984.304| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 4.04 r_work: 0.2496 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14402 Z= 0.142 Angle : 0.604 18.987 19598 Z= 0.284 Chirality : 0.047 0.568 2283 Planarity : 0.003 0.022 2503 Dihedral : 4.883 41.526 2080 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.11 % Allowed : 25.45 % Favored : 71.45 % 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: -0.08 (0.19), residues: 1794 helix: 2.49 (0.29), residues: 330 sheet: -0.14 (0.23), residues: 426 loop : -0.87 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 611 TYR 0.012 0.001 TYR B 208 PHE 0.024 0.001 PHE A 342 TRP 0.007 0.001 TRP B 377 HIS 0.002 0.000 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00319 (14387) covalent geometry : angle 0.53510 (19565) SS BOND : bond 0.00288 ( 12) SS BOND : angle 1.43305 ( 24) hydrogen bonds : bond 0.03727 ( 533) hydrogen bonds : angle 4.75291 ( 1536) link_NAG-ASN : bond 0.01935 ( 3) link_NAG-ASN : angle 12.92614 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.589 Fit side-chains REVERT: A 611 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8233 (mpp80) REVERT: B 266 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8121 (tpp-160) REVERT: B 609 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8930 (mm) outliers start: 47 outliers final: 16 residues processed: 109 average time/residue: 0.3796 time to fit residues: 48.1969 Evaluate side-chains 94 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 627 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 30.0000 chunk 7 optimal weight: 0.0870 chunk 141 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 408 HIS C 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.086913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.048837 restraints weight = 37666.273| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.07 r_work: 0.2529 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14402 Z= 0.098 Angle : 0.581 17.989 19598 Z= 0.274 Chirality : 0.045 0.527 2283 Planarity : 0.003 0.027 2503 Dihedral : 4.485 38.024 2080 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.26 % Allowed : 26.90 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.19), residues: 1794 helix: 2.57 (0.28), residues: 330 sheet: -0.08 (0.23), residues: 426 loop : -0.87 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 611 TYR 0.008 0.001 TYR A 627 PHE 0.019 0.001 PHE A 342 TRP 0.008 0.001 TRP B 377 HIS 0.002 0.000 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00214 (14387) covalent geometry : angle 0.51804 (19565) SS BOND : bond 0.00386 ( 12) SS BOND : angle 1.38740 ( 24) hydrogen bonds : bond 0.03367 ( 533) hydrogen bonds : angle 4.54543 ( 1536) link_NAG-ASN : bond 0.02093 ( 3) link_NAG-ASN : angle 12.13351 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.589 Fit side-chains REVERT: A 611 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8264 (mpp80) REVERT: B 609 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 32 TYR cc_start: 0.8488 (t80) cc_final: 0.8268 (t80) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 0.3921 time to fit residues: 42.5177 Evaluate side-chains 88 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.086612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048578 restraints weight = 37775.427| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.06 r_work: 0.2524 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14402 Z= 0.110 Angle : 0.574 17.424 19598 Z= 0.270 Chirality : 0.045 0.517 2283 Planarity : 0.003 0.031 2503 Dihedral : 4.332 36.579 2080 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.26 % Allowed : 26.90 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.19), residues: 1794 helix: 2.61 (0.29), residues: 330 sheet: -0.05 (0.23), residues: 426 loop : -0.85 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 611 TYR 0.022 0.001 TYR C 36 PHE 0.023 0.001 PHE B 145 TRP 0.006 0.001 TRP B 377 HIS 0.002 0.000 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00247 (14387) covalent geometry : angle 0.51419 (19565) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.42472 ( 24) hydrogen bonds : bond 0.03351 ( 533) hydrogen bonds : angle 4.47795 ( 1536) link_NAG-ASN : bond 0.02008 ( 3) link_NAG-ASN : angle 11.71495 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.599 Fit side-chains REVERT: A 611 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8298 (mpp80) REVERT: B 32 TYR cc_start: 0.8340 (t80) cc_final: 0.8134 (t80) REVERT: B 174 ILE cc_start: 0.8932 (mp) cc_final: 0.8682 (tt) REVERT: B 609 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8945 (mm) REVERT: C 32 TYR cc_start: 0.8488 (t80) cc_final: 0.8269 (t80) REVERT: C 587 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8505 (mtp85) outliers start: 19 outliers final: 10 residues processed: 96 average time/residue: 0.3963 time to fit residues: 44.0214 Evaluate side-chains 91 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.086530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048416 restraints weight = 38023.230| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 4.08 r_work: 0.2514 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14402 Z= 0.122 Angle : 0.574 17.022 19598 Z= 0.272 Chirality : 0.045 0.506 2283 Planarity : 0.003 0.026 2503 Dihedral : 4.282 36.052 2080 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.06 % Allowed : 27.30 % Favored : 71.65 % 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: 0.01 (0.19), residues: 1794 helix: 2.59 (0.29), residues: 330 sheet: -0.04 (0.23), residues: 426 loop : -0.84 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 611 TYR 0.015 0.001 TYR C 36 PHE 0.021 0.001 PHE C 342 TRP 0.006 0.001 TRP C 377 HIS 0.002 0.000 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00276 (14387) covalent geometry : angle 0.51749 (19565) SS BOND : bond 0.00274 ( 12) SS BOND : angle 1.42846 ( 24) hydrogen bonds : bond 0.03373 ( 533) hydrogen bonds : angle 4.46369 ( 1536) link_NAG-ASN : bond 0.01950 ( 3) link_NAG-ASN : angle 11.39604 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.576 Fit side-chains REVERT: A 32 TYR cc_start: 0.8217 (t80) cc_final: 0.8001 (t80) REVERT: A 611 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8307 (mpp80) REVERT: B 174 ILE cc_start: 0.8986 (mp) cc_final: 0.8731 (tt) REVERT: B 609 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8936 (mm) REVERT: C 32 TYR cc_start: 0.8522 (t80) cc_final: 0.8311 (t80) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.3723 time to fit residues: 39.4715 Evaluate side-chains 90 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 57 optimal weight: 0.0070 chunk 115 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.086399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048389 restraints weight = 37851.221| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 4.06 r_work: 0.2515 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14402 Z= 0.127 Angle : 0.579 16.688 19598 Z= 0.273 Chirality : 0.045 0.500 2283 Planarity : 0.003 0.025 2503 Dihedral : 4.234 35.663 2080 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.06 % Allowed : 27.43 % Favored : 71.51 % 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: 0.01 (0.19), residues: 1794 helix: 2.60 (0.29), residues: 330 sheet: -0.04 (0.23), residues: 426 loop : -0.85 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 611 TYR 0.010 0.001 TYR C 36 PHE 0.023 0.001 PHE B 145 TRP 0.007 0.001 TRP C 377 HIS 0.002 0.000 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00289 (14387) covalent geometry : angle 0.52536 (19565) SS BOND : bond 0.00274 ( 12) SS BOND : angle 1.42010 ( 24) hydrogen bonds : bond 0.03404 ( 533) hydrogen bonds : angle 4.44396 ( 1536) link_NAG-ASN : bond 0.01929 ( 3) link_NAG-ASN : angle 11.14652 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 611 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8299 (mpp80) REVERT: B 174 ILE cc_start: 0.8955 (mp) cc_final: 0.8692 (tt) REVERT: B 609 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8934 (mm) REVERT: C 32 TYR cc_start: 0.8545 (t80) cc_final: 0.8305 (t80) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.4158 time to fit residues: 44.1575 Evaluate side-chains 90 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 0.0570 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 103 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.086601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.048616 restraints weight = 37777.262| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 4.05 r_work: 0.2527 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14402 Z= 0.110 Angle : 0.572 16.343 19598 Z= 0.270 Chirality : 0.045 0.494 2283 Planarity : 0.003 0.025 2503 Dihedral : 4.165 34.920 2080 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.99 % Allowed : 27.76 % Favored : 71.25 % 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: 0.02 (0.19), residues: 1794 helix: 2.62 (0.29), residues: 330 sheet: -0.02 (0.23), residues: 426 loop : -0.85 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 611 TYR 0.011 0.001 TYR C 36 PHE 0.021 0.001 PHE A 342 TRP 0.007 0.001 TRP C 377 HIS 0.002 0.000 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00249 (14387) covalent geometry : angle 0.52025 (19565) SS BOND : bond 0.00284 ( 12) SS BOND : angle 1.38925 ( 24) hydrogen bonds : bond 0.03309 ( 533) hydrogen bonds : angle 4.38866 ( 1536) link_NAG-ASN : bond 0.01964 ( 3) link_NAG-ASN : angle 10.90218 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4664.96 seconds wall clock time: 80 minutes 37.24 seconds (4837.24 seconds total)