Starting phenix.real_space_refine on Wed Mar 4 10:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd7_30647/03_2026/7dd7_30647.map" } resolution = 3.2 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= -0.001 sd= 0.051 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 2 4.86 5 C 8262 2.51 5 N 2033 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12737 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6212 Classifications: {'peptide': 791} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6235 Classifications: {'peptide': 792} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {' CA': 2, ' CL': 1, 'H43': 1, 'NAG': 3} Inner-chain residues flagged as termini: ['pdbres="TRP A1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' CA': 4, ' CL': 1, 'H43': 1, 'NAG': 3} Inner-chain residues flagged as termini: ['pdbres="TRP B1109 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12737 At special positions: 0 Unit cell: (105.456, 96.33, 183.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 70 16.00 O 2364 8.00 N 2033 7.00 C 8262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.73 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.24 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.13 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.66 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=1.99 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1104 " - " ASN A 287 " " NAG A1105 " - " ASN A 399 " " NAG A1106 " - " ASN A 467 " " NAG B1106 " - " ASN B 287 " " NAG B1107 " - " ASN B 399 " " NAG B1108 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 482.6 milliseconds 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 49.7% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.641A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.713A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.707A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.560A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.387A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.779A pdb=" N VAL A 403 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.594A pdb=" N LYS A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 454 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.525A pdb=" N HIS A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 609 through 637 Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.807A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.951A pdb=" N SER A 664 " --> pdb=" O CYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 672 through 697 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 720 through 744 removed outlier: 4.223A pdb=" N PHE A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 734 " --> pdb=" O CYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 793 removed outlier: 3.658A pdb=" N SER A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 removed outlier: 4.014A pdb=" N PHE A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Proline residue: A 822 - end of helix Processing helix chain 'A' and resid 828 through 862 removed outlier: 5.461A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.727A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.027A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.643A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.530A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.912A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.501A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.702A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.734A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.621A pdb=" N LYS B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 454' Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.616A pdb=" N HIS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 637 Processing helix chain 'B' and resid 639 through 644 removed outlier: 3.807A pdb=" N LYS B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.952A pdb=" N SER B 664 " --> pdb=" O CYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 672 through 698 Proline residue: B 681 - end of helix removed outlier: 3.562A pdb=" N THR B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 720 through 744 removed outlier: 4.223A pdb=" N PHE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 734 " --> pdb=" O CYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 793 removed outlier: 3.659A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 4.015A pdb=" N PHE B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 828 through 862 removed outlier: 5.461A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.103A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.819A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.983A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 488 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS A 509 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 490 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'A' and resid 601 through 603 Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.971A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.850A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.918A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 317 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 488 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS B 509 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 490 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB4, first strand: chain 'B' and resid 549 through 552 Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AB6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 603 601 hydrogen bonds defined for protein. 1749 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: 2.23 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2065 1.31 - 1.44: 3672 1.44 - 1.57: 7224 1.57 - 1.70: 9 1.70 - 1.83: 86 Bond restraints: 13056 Sorted by residual: bond pdb=" C10 H43 B1110 " pdb=" C11 H43 B1110 " ideal model delta sigma weight residual 1.528 1.341 0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C10 H43 A1108 " pdb=" C11 H43 A1108 " ideal model delta sigma weight residual 1.528 1.341 0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C25 H43 B1110 " pdb=" C26 H43 B1110 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C25 H43 A1108 " pdb=" C26 H43 A1108 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C26 H43 A1108 " pdb=" N9 H43 A1108 " ideal model delta sigma weight residual 1.449 1.585 -0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 13051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 17495 3.17 - 6.33: 208 6.33 - 9.50: 20 9.50 - 12.67: 5 12.67 - 15.83: 3 Bond angle restraints: 17731 Sorted by residual: angle pdb=" N GLU A 603 " pdb=" CA GLU A 603 " pdb=" C GLU A 603 " ideal model delta sigma weight residual 109.25 122.61 -13.36 1.53e+00 4.27e-01 7.63e+01 angle pdb=" C ILE A 598 " pdb=" N PRO A 599 " pdb=" CA PRO A 599 " ideal model delta sigma weight residual 119.90 127.96 -8.06 1.02e+00 9.61e-01 6.24e+01 angle pdb=" N ILE A 598 " pdb=" CA ILE A 598 " pdb=" C ILE A 598 " ideal model delta sigma weight residual 109.02 102.43 6.59 9.30e-01 1.16e+00 5.03e+01 angle pdb=" C10 H43 B1110 " pdb=" N9 H43 B1110 " pdb=" C8 H43 B1110 " ideal model delta sigma weight residual 123.60 107.77 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C10 H43 A1108 " pdb=" N9 H43 A1108 " pdb=" C8 H43 A1108 " ideal model delta sigma weight residual 123.60 107.78 15.82 3.00e+00 1.11e-01 2.78e+01 ... (remaining 17726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 7327 23.35 - 46.70: 429 46.70 - 70.06: 72 70.06 - 93.41: 26 93.41 - 116.76: 7 Dihedral angle restraints: 7861 sinusoidal: 3257 harmonic: 4604 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual 93.00 16.56 76.44 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS A 545 " pdb=" SG CYS A 545 " pdb=" SG CYS A 564 " pdb=" CB CYS A 564 " ideal model delta sinusoidal sigma weight residual 93.00 158.85 -65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 7858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1917 0.105 - 0.211: 82 0.211 - 0.316: 7 0.316 - 0.421: 2 0.421 - 0.526: 1 Chirality restraints: 2009 Sorted by residual: 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 -2.34 -0.06 2.00e-02 2.50e+03 8.36e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA CYS B 597 " pdb=" N CYS B 597 " pdb=" C CYS B 597 " pdb=" CB CYS B 597 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2006 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 696 " -0.028 2.00e-02 2.50e+03 5.54e-02 3.07e+01 pdb=" C VAL A 696 " 0.096 2.00e-02 2.50e+03 pdb=" O VAL A 696 " -0.036 2.00e-02 2.50e+03 pdb=" N LYS A 697 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 599 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C PRO A 599 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO A 599 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS A 600 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 696 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL B 696 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL B 696 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 697 " 0.020 2.00e-02 2.50e+03 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 64 2.40 - 3.02: 8726 3.02 - 3.65: 18470 3.65 - 4.27: 28125 4.27 - 4.90: 45964 Nonbonded interactions: 101349 Sorted by model distance: nonbonded pdb=" O GLN B 601 " pdb=" CG2 ILE B 759 " model vdw 1.770 3.460 nonbonded pdb=" CE2 TYR B 572 " pdb=" SG CYS B 584 " model vdw 1.854 3.700 nonbonded pdb=" O LEU B 630 " pdb=" NH2 ARG B 637 " model vdw 1.979 3.120 nonbonded pdb=" O LEU A 630 " pdb=" NH2 ARG A 637 " model vdw 1.980 3.120 nonbonded pdb=" OG1 THR A 634 " pdb=" NH2 ARG A 637 " model vdw 2.061 3.120 ... (remaining 101344 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 22 through 119 or resid 136 through 698 or (resid 699 thro \ ugh 718 and (name N or name CA or name C or name O or name CB )) or resid 719 th \ rough 867 or resid 1103 or resid 1106 through 1108)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 867 or \ resid 1103 or resid 1106 or resid 1109 through 1110)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.640 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.560 Find NCS groups from input model: 0.260 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 0.700 13085 Z= 0.666 Angle : 1.028 49.617 17803 Z= 0.555 Chirality : 0.053 0.526 2009 Planarity : 0.005 0.055 2236 Dihedral : 15.844 116.758 4836 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 39.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.30 % Allowed : 14.17 % Favored : 85.53 % 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 are not related in a simple way. whole: -3.39 (0.17), residues: 1567 helix: -1.65 (0.16), residues: 703 sheet: -2.08 (0.38), residues: 151 loop : -2.89 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.007 0.001 TYR A 203 PHE 0.025 0.002 PHE B 814 TRP 0.034 0.002 TRP A 817 HIS 0.004 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00987 (13056) covalent geometry : angle 0.87569 (17731) SS BOND : bond 0.25044 ( 15) SS BOND : angle 12.69609 ( 30) hydrogen bonds : bond 0.15434 ( 601) hydrogen bonds : angle 7.09595 ( 1749) link_BETA1-4 : bond 0.00459 ( 4) link_BETA1-4 : angle 1.06896 ( 12) link_NAG-ASN : bond 0.00407 ( 10) link_NAG-ASN : angle 3.51294 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 301 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.7922 (mp) cc_final: 0.7669 (tp) REVERT: A 805 PHE cc_start: 0.7161 (m-80) cc_final: 0.6790 (m-80) REVERT: A 824 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.5419 (t80) REVERT: B 522 ILE cc_start: 0.8946 (mt) cc_final: 0.8744 (mt) REVERT: B 805 PHE cc_start: 0.8948 (m-80) cc_final: 0.8649 (m-80) outliers start: 4 outliers final: 0 residues processed: 305 average time/residue: 0.1388 time to fit residues: 57.8660 Evaluate side-chains 161 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 824 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 83 ASN A 193 GLN A 335 GLN A 338 HIS A 465 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 193 GLN B 260 GLN B 335 GLN B 465 HIS B 475 GLN B 494 HIS ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105359 restraints weight = 19128.931| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.26 r_work: 0.3248 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13085 Z= 0.173 Angle : 0.780 14.512 17803 Z= 0.384 Chirality : 0.051 0.691 2009 Planarity : 0.005 0.043 2236 Dihedral : 10.694 109.598 2011 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.60 % Allowed : 17.06 % Favored : 80.34 % 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 are not related in a simple way. whole: -1.81 (0.20), residues: 1567 helix: -0.23 (0.19), residues: 714 sheet: -1.56 (0.38), residues: 177 loop : -2.14 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 751 TYR 0.022 0.002 TYR B 651 PHE 0.035 0.002 PHE B 683 TRP 0.032 0.001 TRP A 817 HIS 0.007 0.001 HIS A 753 Details of bonding type rmsd covalent geometry : bond 0.00363 (13056) covalent geometry : angle 0.76099 (17731) SS BOND : bond 0.00960 ( 15) SS BOND : angle 1.78473 ( 30) hydrogen bonds : bond 0.06112 ( 601) hydrogen bonds : angle 5.58247 ( 1749) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 1.47637 ( 12) link_NAG-ASN : bond 0.00505 ( 10) link_NAG-ASN : angle 3.84604 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.7938 (mp) cc_final: 0.7651 (tp) REVERT: A 338 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7265 (t-90) REVERT: A 518 GLU cc_start: 0.7400 (tp30) cc_final: 0.7143 (tp30) REVERT: A 805 PHE cc_start: 0.7219 (m-80) cc_final: 0.6803 (m-80) REVERT: A 808 PHE cc_start: 0.5240 (OUTLIER) cc_final: 0.4622 (m-80) REVERT: B 205 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7922 (mtp85) REVERT: B 231 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 805 PHE cc_start: 0.9079 (m-80) cc_final: 0.8621 (m-80) REVERT: B 810 MET cc_start: 0.6678 (mtm) cc_final: 0.6425 (mtm) REVERT: B 813 PHE cc_start: 0.7809 (t80) cc_final: 0.7533 (t80) outliers start: 35 outliers final: 14 residues processed: 215 average time/residue: 0.0952 time to fit residues: 31.0014 Evaluate side-chains 166 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 832 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 475 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.158190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104880 restraints weight = 19193.541| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.23 r_work: 0.3255 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13085 Z= 0.153 Angle : 0.687 14.881 17803 Z= 0.339 Chirality : 0.049 0.685 2009 Planarity : 0.004 0.043 2236 Dihedral : 9.285 107.295 2009 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 18.32 % Favored : 78.93 % 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 are not related in a simple way. whole: -1.19 (0.20), residues: 1567 helix: 0.33 (0.19), residues: 713 sheet: -1.39 (0.40), residues: 167 loop : -1.83 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 227 TYR 0.017 0.001 TYR B 651 PHE 0.022 0.001 PHE B 845 TRP 0.034 0.002 TRP B 607 HIS 0.008 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00335 (13056) covalent geometry : angle 0.66353 (17731) SS BOND : bond 0.00561 ( 15) SS BOND : angle 1.45623 ( 30) hydrogen bonds : bond 0.05418 ( 601) hydrogen bonds : angle 5.28193 ( 1749) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 1.54544 ( 12) link_NAG-ASN : bond 0.00437 ( 10) link_NAG-ASN : angle 4.06057 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8108 (mp) cc_final: 0.7745 (tp) REVERT: A 605 LEU cc_start: 0.8729 (mp) cc_final: 0.8527 (mp) REVERT: A 805 PHE cc_start: 0.7343 (m-80) cc_final: 0.6931 (m-80) REVERT: A 808 PHE cc_start: 0.5215 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: B 205 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7966 (mtp85) REVERT: B 228 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 231 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 770 MET cc_start: 0.5427 (mtm) cc_final: 0.5163 (mpp) REVERT: B 786 CYS cc_start: 0.8557 (t) cc_final: 0.7932 (p) REVERT: B 802 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 805 PHE cc_start: 0.9101 (m-80) cc_final: 0.8578 (m-80) outliers start: 37 outliers final: 23 residues processed: 173 average time/residue: 0.0889 time to fit residues: 24.1381 Evaluate side-chains 160 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 HIS ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100776 restraints weight = 19314.923| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.14 r_work: 0.3190 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13085 Z= 0.215 Angle : 0.691 16.082 17803 Z= 0.348 Chirality : 0.051 0.731 2009 Planarity : 0.004 0.043 2236 Dihedral : 8.846 105.012 2009 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.08 % Allowed : 17.66 % Favored : 78.26 % 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 are not related in a simple way. whole: -0.94 (0.20), residues: 1567 helix: 0.47 (0.19), residues: 711 sheet: -1.26 (0.39), residues: 167 loop : -1.60 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 751 TYR 0.019 0.002 TYR A 434 PHE 0.025 0.002 PHE B 845 TRP 0.031 0.002 TRP A 817 HIS 0.007 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00496 (13056) covalent geometry : angle 0.66985 (17731) SS BOND : bond 0.00444 ( 15) SS BOND : angle 1.43790 ( 30) hydrogen bonds : bond 0.05508 ( 601) hydrogen bonds : angle 5.22908 ( 1749) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 1.65393 ( 12) link_NAG-ASN : bond 0.00392 ( 10) link_NAG-ASN : angle 3.90636 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 668 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6344 (mp) REVERT: A 805 PHE cc_start: 0.7398 (m-80) cc_final: 0.7030 (m-80) REVERT: A 808 PHE cc_start: 0.5593 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: B 205 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7993 (mtp85) REVERT: B 228 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 231 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 560 CYS cc_start: 0.5610 (m) cc_final: 0.5090 (m) REVERT: B 668 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5486 (mm) REVERT: B 786 CYS cc_start: 0.8798 (t) cc_final: 0.8352 (p) REVERT: B 805 PHE cc_start: 0.9043 (m-80) cc_final: 0.8612 (m-80) REVERT: B 850 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6293 (p) outliers start: 55 outliers final: 36 residues processed: 189 average time/residue: 0.0980 time to fit residues: 28.5967 Evaluate side-chains 175 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 84 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 734 GLN ** 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 = 0.4094 r_free = 0.4094 target = 0.155813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101955 restraints weight = 19315.992| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.25 r_work: 0.3198 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13085 Z= 0.136 Angle : 0.639 15.328 17803 Z= 0.318 Chirality : 0.048 0.704 2009 Planarity : 0.004 0.044 2236 Dihedral : 8.607 104.642 2009 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.26 % Allowed : 19.21 % Favored : 77.52 % 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 are not related in a simple way. whole: -0.71 (0.20), residues: 1567 helix: 0.64 (0.19), residues: 712 sheet: -1.12 (0.39), residues: 164 loop : -1.48 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 227 TYR 0.012 0.001 TYR A 434 PHE 0.022 0.001 PHE B 845 TRP 0.028 0.002 TRP B 607 HIS 0.027 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00299 (13056) covalent geometry : angle 0.61888 (17731) SS BOND : bond 0.00242 ( 15) SS BOND : angle 1.03372 ( 30) hydrogen bonds : bond 0.04830 ( 601) hydrogen bonds : angle 5.04699 ( 1749) link_BETA1-4 : bond 0.00334 ( 4) link_BETA1-4 : angle 1.58274 ( 12) link_NAG-ASN : bond 0.00474 ( 10) link_NAG-ASN : angle 3.72934 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 228 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 668 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6444 (mp) REVERT: A 805 PHE cc_start: 0.7393 (m-80) cc_final: 0.7029 (m-80) REVERT: A 808 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.5071 (m-80) REVERT: B 205 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7941 (mtp85) REVERT: B 229 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7710 (mt-10) REVERT: B 231 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 560 CYS cc_start: 0.5649 (m) cc_final: 0.5303 (m) REVERT: B 584 CYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6597 (m) REVERT: B 786 CYS cc_start: 0.8906 (t) cc_final: 0.8390 (p) REVERT: B 805 PHE cc_start: 0.9047 (m-80) cc_final: 0.8637 (m-80) REVERT: B 850 CYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6219 (p) outliers start: 44 outliers final: 29 residues processed: 172 average time/residue: 0.0955 time to fit residues: 25.7806 Evaluate side-chains 159 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 65 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.0020 chunk 68 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.156449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102980 restraints weight = 19283.445| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.23 r_work: 0.3215 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13085 Z= 0.126 Angle : 0.619 14.972 17803 Z= 0.308 Chirality : 0.047 0.685 2009 Planarity : 0.004 0.043 2236 Dihedral : 8.394 102.995 2009 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.86 % Allowed : 18.99 % Favored : 77.15 % 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 are not related in a simple way. whole: -0.55 (0.21), residues: 1567 helix: 0.75 (0.19), residues: 709 sheet: -1.02 (0.40), residues: 164 loop : -1.36 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 227 TYR 0.016 0.001 TYR A 434 PHE 0.019 0.001 PHE B 813 TRP 0.026 0.001 TRP A 817 HIS 0.003 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00276 (13056) covalent geometry : angle 0.59918 (17731) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.96207 ( 30) hydrogen bonds : bond 0.04515 ( 601) hydrogen bonds : angle 4.94130 ( 1749) link_BETA1-4 : bond 0.00324 ( 4) link_BETA1-4 : angle 1.60585 ( 12) link_NAG-ASN : bond 0.00399 ( 10) link_NAG-ASN : angle 3.60464 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 228 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 338 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7223 (t-90) REVERT: A 588 TYR cc_start: 0.7934 (m-80) cc_final: 0.7659 (m-80) REVERT: A 805 PHE cc_start: 0.7339 (m-80) cc_final: 0.6982 (m-80) REVERT: A 808 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.4826 (m-80) REVERT: B 205 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7921 (mtp85) REVERT: B 229 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7754 (mt-10) REVERT: B 231 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 584 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.7002 (m) REVERT: B 607 TRP cc_start: 0.8425 (m100) cc_final: 0.8152 (m100) REVERT: B 786 CYS cc_start: 0.8949 (t) cc_final: 0.8705 (t) REVERT: B 805 PHE cc_start: 0.9035 (m-80) cc_final: 0.8636 (m-80) REVERT: B 810 MET cc_start: 0.7088 (mtm) cc_final: 0.6641 (mtm) REVERT: B 850 CYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6179 (p) outliers start: 52 outliers final: 35 residues processed: 180 average time/residue: 0.0996 time to fit residues: 28.6758 Evaluate side-chains 172 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.153817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100067 restraints weight = 19410.805| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.22 r_work: 0.3202 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13085 Z= 0.182 Angle : 0.645 15.590 17803 Z= 0.325 Chirality : 0.049 0.710 2009 Planarity : 0.004 0.044 2236 Dihedral : 8.354 102.107 2009 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.93 % Allowed : 20.18 % Favored : 75.89 % 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 are not related in a simple way. whole: -0.45 (0.21), residues: 1567 helix: 0.82 (0.19), residues: 705 sheet: -0.90 (0.40), residues: 162 loop : -1.29 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 227 TYR 0.018 0.001 TYR A 434 PHE 0.019 0.001 PHE B 666 TRP 0.034 0.002 TRP A 817 HIS 0.007 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00423 (13056) covalent geometry : angle 0.62502 (17731) SS BOND : bond 0.00293 ( 15) SS BOND : angle 1.09460 ( 30) hydrogen bonds : bond 0.04831 ( 601) hydrogen bonds : angle 4.95370 ( 1749) link_BETA1-4 : bond 0.00253 ( 4) link_BETA1-4 : angle 1.67143 ( 12) link_NAG-ASN : bond 0.00341 ( 10) link_NAG-ASN : angle 3.70255 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 202 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 228 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 338 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7382 (t-90) REVERT: A 805 PHE cc_start: 0.7344 (m-80) cc_final: 0.6977 (m-80) REVERT: A 808 PHE cc_start: 0.5151 (OUTLIER) cc_final: 0.4699 (m-80) REVERT: B 205 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7943 (mtp85) REVERT: B 229 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7778 (mt-10) REVERT: B 231 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 253 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 545 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7002 (m) REVERT: B 601 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7292 (tp-100) REVERT: B 607 TRP cc_start: 0.8416 (m100) cc_final: 0.8119 (m100) REVERT: B 805 PHE cc_start: 0.9104 (m-80) cc_final: 0.8740 (m-80) REVERT: B 850 CYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6346 (p) outliers start: 53 outliers final: 37 residues processed: 176 average time/residue: 0.0942 time to fit residues: 26.3884 Evaluate side-chains 170 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** 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 = 0.4079 r_free = 0.4079 target = 0.153935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100219 restraints weight = 19300.177| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.21 r_work: 0.3170 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13085 Z= 0.175 Angle : 0.644 15.550 17803 Z= 0.324 Chirality : 0.049 0.710 2009 Planarity : 0.004 0.043 2236 Dihedral : 8.298 101.855 2009 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.71 % Allowed : 20.70 % Favored : 75.59 % 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 are not related in a simple way. whole: -0.38 (0.21), residues: 1567 helix: 0.88 (0.19), residues: 705 sheet: -0.86 (0.40), residues: 163 loop : -1.27 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 227 TYR 0.019 0.001 TYR A 434 PHE 0.019 0.001 PHE B 666 TRP 0.027 0.002 TRP A 817 HIS 0.005 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00405 (13056) covalent geometry : angle 0.62129 (17731) SS BOND : bond 0.00266 ( 15) SS BOND : angle 1.12379 ( 30) hydrogen bonds : bond 0.04784 ( 601) hydrogen bonds : angle 4.95817 ( 1749) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 1.65641 ( 12) link_NAG-ASN : bond 0.00956 ( 10) link_NAG-ASN : angle 3.99759 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 202 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: A 228 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 338 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7406 (t-90) REVERT: A 607 TRP cc_start: 0.7812 (m100) cc_final: 0.7500 (m-10) REVERT: A 805 PHE cc_start: 0.7529 (m-80) cc_final: 0.7096 (m-80) REVERT: A 808 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: B 205 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7933 (mtp85) REVERT: B 229 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7737 (mt-10) REVERT: B 231 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 545 CYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6994 (m) REVERT: B 560 CYS cc_start: 0.5870 (m) cc_final: 0.5551 (m) REVERT: B 601 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7403 (tp-100) REVERT: B 607 TRP cc_start: 0.8346 (m100) cc_final: 0.8060 (m100) REVERT: B 786 CYS cc_start: 0.9122 (t) cc_final: 0.8574 (p) REVERT: B 805 PHE cc_start: 0.9074 (m-80) cc_final: 0.8718 (m-80) REVERT: B 850 CYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6240 (p) outliers start: 50 outliers final: 39 residues processed: 172 average time/residue: 0.0929 time to fit residues: 25.2611 Evaluate side-chains 174 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 338 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.155018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101851 restraints weight = 19200.838| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.21 r_work: 0.3194 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13085 Z= 0.138 Angle : 0.644 15.099 17803 Z= 0.321 Chirality : 0.048 0.684 2009 Planarity : 0.004 0.041 2236 Dihedral : 8.172 100.861 2009 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.64 % Allowed : 21.36 % Favored : 75.00 % 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 are not related in a simple way. whole: -0.27 (0.21), residues: 1567 helix: 0.98 (0.19), residues: 705 sheet: -0.90 (0.40), residues: 164 loop : -1.18 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 227 TYR 0.025 0.001 TYR A 434 PHE 0.021 0.001 PHE B 813 TRP 0.025 0.001 TRP A 817 HIS 0.005 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00312 (13056) covalent geometry : angle 0.62276 (17731) SS BOND : bond 0.00240 ( 15) SS BOND : angle 1.02146 ( 30) hydrogen bonds : bond 0.04502 ( 601) hydrogen bonds : angle 4.89632 ( 1749) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.62312 ( 12) link_NAG-ASN : bond 0.00613 ( 10) link_NAG-ASN : angle 3.80847 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8189 (tt) REVERT: A 202 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: A 338 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7437 (t-90) REVERT: A 588 TYR cc_start: 0.8029 (m-80) cc_final: 0.7701 (m-80) REVERT: A 607 TRP cc_start: 0.7788 (m100) cc_final: 0.7503 (m-10) REVERT: A 805 PHE cc_start: 0.7510 (m-80) cc_final: 0.7088 (m-80) REVERT: A 808 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4892 (m-80) REVERT: B 205 ARG cc_start: 0.8393 (mtt90) cc_final: 0.7971 (mtp85) REVERT: B 229 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7716 (mt-10) REVERT: B 231 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 251 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 545 CYS cc_start: 0.7262 (OUTLIER) cc_final: 0.7032 (m) REVERT: B 560 CYS cc_start: 0.5872 (m) cc_final: 0.5587 (m) REVERT: B 601 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7489 (tp-100) REVERT: B 607 TRP cc_start: 0.8308 (m100) cc_final: 0.8020 (m-90) REVERT: B 786 CYS cc_start: 0.9060 (t) cc_final: 0.8464 (p) REVERT: B 805 PHE cc_start: 0.9097 (m-80) cc_final: 0.8525 (m-80) REVERT: B 850 CYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6396 (p) outliers start: 49 outliers final: 38 residues processed: 178 average time/residue: 0.0930 time to fit residues: 26.1965 Evaluate side-chains 171 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 253 GLN B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102020 restraints weight = 19329.075| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.21 r_work: 0.3198 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13085 Z= 0.134 Angle : 0.641 14.915 17803 Z= 0.320 Chirality : 0.048 0.677 2009 Planarity : 0.004 0.040 2236 Dihedral : 8.044 99.043 2009 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.86 % Allowed : 21.07 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1567 helix: 1.08 (0.19), residues: 702 sheet: -0.87 (0.40), residues: 164 loop : -1.12 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 519 TYR 0.024 0.001 TYR A 434 PHE 0.021 0.001 PHE B 666 TRP 0.022 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00303 (13056) covalent geometry : angle 0.62024 (17731) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.94852 ( 30) hydrogen bonds : bond 0.04424 ( 601) hydrogen bonds : angle 4.83059 ( 1749) link_BETA1-4 : bond 0.00301 ( 4) link_BETA1-4 : angle 1.60609 ( 12) link_NAG-ASN : bond 0.00597 ( 10) link_NAG-ASN : angle 3.79985 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 202 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 338 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: A 480 GLU cc_start: 0.8203 (pm20) cc_final: 0.7997 (tm-30) REVERT: A 588 TYR cc_start: 0.8023 (m-80) cc_final: 0.7686 (m-80) REVERT: A 607 TRP cc_start: 0.7806 (m100) cc_final: 0.7476 (m-10) REVERT: A 805 PHE cc_start: 0.7524 (m-80) cc_final: 0.7093 (m-80) REVERT: A 808 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: A 814 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: B 205 ARG cc_start: 0.8396 (mtt90) cc_final: 0.7966 (mtp85) REVERT: B 229 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7696 (mt-10) REVERT: B 231 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 251 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 545 CYS cc_start: 0.7261 (OUTLIER) cc_final: 0.7052 (m) REVERT: B 560 CYS cc_start: 0.5950 (m) cc_final: 0.5678 (m) REVERT: B 601 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7500 (tp-100) REVERT: B 607 TRP cc_start: 0.8347 (m100) cc_final: 0.8091 (m-90) REVERT: B 786 CYS cc_start: 0.9125 (t) cc_final: 0.8542 (p) REVERT: B 805 PHE cc_start: 0.9106 (m-80) cc_final: 0.8518 (m-80) REVERT: B 850 CYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6400 (p) outliers start: 52 outliers final: 40 residues processed: 175 average time/residue: 0.0915 time to fit residues: 25.7548 Evaluate side-chains 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098860 restraints weight = 19332.968| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.11 r_work: 0.3152 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13085 Z= 0.232 Angle : 0.695 16.291 17803 Z= 0.351 Chirality : 0.051 0.747 2009 Planarity : 0.004 0.041 2236 Dihedral : 8.206 99.468 2009 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.49 % Allowed : 21.36 % Favored : 75.15 % 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 are not related in a simple way. whole: -0.28 (0.21), residues: 1567 helix: 0.99 (0.19), residues: 701 sheet: -0.92 (0.40), residues: 165 loop : -1.20 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 519 TYR 0.028 0.002 TYR A 434 PHE 0.022 0.002 PHE B 813 TRP 0.023 0.002 TRP A 817 HIS 0.006 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00547 (13056) covalent geometry : angle 0.67324 (17731) SS BOND : bond 0.00393 ( 15) SS BOND : angle 1.30882 ( 30) hydrogen bonds : bond 0.05129 ( 601) hydrogen bonds : angle 5.00076 ( 1749) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.68724 ( 12) link_NAG-ASN : bond 0.00531 ( 10) link_NAG-ASN : angle 4.00699 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.00 seconds wall clock time: 61 minutes 33.43 seconds (3693.43 seconds total)