Starting phenix.real_space_refine on Mon Jul 28 18:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.map" model { file = "/net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mtq_23994/07_2025/7mtq_23994.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6603 2.51 5 N 1778 2.21 5 O 1949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5132 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 34, 'TRANS': 707} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 586 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 3, 'PHE:plan': 12, 'GLU:plan': 17, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 425 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5176 Classifications: {'peptide': 744} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 36, 'TRANS': 707} Chain breaks: 15 Unresolved non-hydrogen bonds: 652 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 13, 'GLU:plan': 16, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 389 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.92, per 1000 atoms: 0.76 Number of scatterers: 10388 At special positions: 0 Unit cell: (91.1085, 124.949, 186.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1949 8.00 N 1778 7.00 C 6603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 721 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG B 902 " - " ASN B 203 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2786 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 51.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 54 through 74 removed outlier: 4.307A pdb=" N GLN A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 removed outlier: 4.679A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.651A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.775A pdb=" N ALA A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 3.760A pdb=" N GLU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 4.415A pdb=" N LYS A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 324 through 333 removed outlier: 4.023A pdb=" N ALA A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.629A pdb=" N ALA A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 566 through 592 removed outlier: 4.213A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 603 through 624 removed outlier: 4.061A pdb=" N THR A 620 " --> pdb=" O CYS A 616 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 659 removed outlier: 3.540A pdb=" N LEU A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 701 removed outlier: 3.844A pdb=" N VAL A 680 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.568A pdb=" N MET A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.770A pdb=" N LYS A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 757 through 784 Proline residue: A 778 - end of helix removed outlier: 3.639A pdb=" N TYR A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 818 Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 58 through 75 Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.923A pdb=" N LEU B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 4.477A pdb=" N LEU B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.669A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 173 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 174 " --> pdb=" O LYS B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 174' Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.658A pdb=" N LYS B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 231 removed outlier: 3.510A pdb=" N GLY B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.858A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.586A pdb=" N PHE B 348 " --> pdb=" O TRP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 400 removed outlier: 3.730A pdb=" N VAL B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.660A pdb=" N ARG B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 423 through 426 removed outlier: 3.843A pdb=" N VAL B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.543A pdb=" N LEU B 484 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 485 " --> pdb=" O THR B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.848A pdb=" N HIS B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 624 removed outlier: 3.518A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 657 removed outlier: 3.679A pdb=" N LEU B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLY B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 650 " --> pdb=" O CYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 701 removed outlier: 3.899A pdb=" N VAL B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 749 removed outlier: 3.540A pdb=" N THR B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 784 removed outlier: 4.540A pdb=" N PHE B 761 " --> pdb=" O ASN B 757 " (cutoff:3.500A) Proline residue: B 778 - end of helix Processing helix chain 'B' and resid 786 through 819 removed outlier: 3.624A pdb=" N THR B 791 " --> pdb=" O TYR B 787 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 792 " --> pdb=" O ARG B 788 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.516A pdb=" N ALA A 86 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 138 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN A 162 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 241 removed outlier: 7.638A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR A 206 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 267 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER A 208 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE A 269 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 210 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 429 removed outlier: 3.755A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.650A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 33 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ILE B 163 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 234 through 238 removed outlier: 7.559A pdb=" N VAL B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER B 238 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 209 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE B 269 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 210 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP B 291 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE B 317 " --> pdb=" O TRP B 291 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA B 293 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N LEU B 319 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 453 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR B 473 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 455 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 467 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 428 through 429 removed outlier: 3.705A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 509 through 510 547 hydrogen bonds defined for protein. 1620 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: 3.03 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 4350 1.40 - 1.61: 6174 1.61 - 1.83: 75 1.83 - 2.04: 0 2.04 - 2.26: 1 Bond restraints: 10600 Sorted by residual: bond pdb=" C GLN A 526 " pdb=" N TYR A 528 " ideal model delta sigma weight residual 1.332 2.256 -0.923 1.40e-02 5.10e+03 4.35e+03 bond pdb=" CAT Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.364 1.489 -0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CAT Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.364 1.489 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" CAS Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.369 1.489 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CAS Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.369 1.488 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 10595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 14306 3.16 - 6.32: 173 6.32 - 9.48: 21 9.48 - 12.64: 5 12.64 - 15.80: 3 Bond angle restraints: 14508 Sorted by residual: angle pdb=" O GLN A 526 " pdb=" C GLN A 526 " pdb=" N TYR A 528 " ideal model delta sigma weight residual 122.59 106.79 15.80 1.33e+00 5.65e-01 1.41e+02 angle pdb=" N ARG A 284 " pdb=" CA ARG A 284 " pdb=" C ARG A 284 " ideal model delta sigma weight residual 111.28 100.79 10.49 1.09e+00 8.42e-01 9.26e+01 angle pdb=" CA GLN A 526 " pdb=" C GLN A 526 " pdb=" N TYR A 528 " ideal model delta sigma weight residual 116.84 102.69 14.15 1.71e+00 3.42e-01 6.85e+01 angle pdb=" C GLN A 526 " pdb=" N TYR A 528 " pdb=" CA TYR A 528 " ideal model delta sigma weight residual 121.54 135.19 -13.65 1.91e+00 2.74e-01 5.10e+01 angle pdb=" N GLN A 283 " pdb=" CA GLN A 283 " pdb=" C GLN A 283 " ideal model delta sigma weight residual 113.43 104.62 8.81 1.26e+00 6.30e-01 4.89e+01 ... (remaining 14503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 5896 24.54 - 49.09: 332 49.09 - 73.63: 34 73.63 - 98.17: 3 98.17 - 122.72: 2 Dihedral angle restraints: 6267 sinusoidal: 1978 harmonic: 4289 Sorted by residual: dihedral pdb=" CB CYS A 504 " pdb=" SG CYS A 504 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -172.91 86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 14.33 78.67 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CA ARG B 411 " pdb=" C ARG B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 6264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1543 0.078 - 0.157: 154 0.157 - 0.235: 15 0.235 - 0.313: 10 0.313 - 0.392: 5 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA VAL B 700 " pdb=" N VAL B 700 " pdb=" C VAL B 700 " pdb=" CB VAL B 700 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA TRP B 487 " pdb=" N TRP B 487 " pdb=" C TRP B 487 " pdb=" CB TRP B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ILE B 485 " pdb=" N ILE B 485 " pdb=" C ILE B 485 " pdb=" CB ILE B 485 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1724 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 526 " 0.134 2.00e-02 2.50e+03 2.27e-01 5.14e+02 pdb=" C GLN A 526 " -0.386 2.00e-02 2.50e+03 pdb=" O GLN A 526 " 0.185 2.00e-02 2.50e+03 pdb=" N TYR A 528 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 698 " -0.025 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C LEU A 698 " 0.093 2.00e-02 2.50e+03 pdb=" O LEU A 698 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL A 699 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 411 " -0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO B 412 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.048 5.00e-02 4.00e+02 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1328 2.74 - 3.28: 10180 3.28 - 3.82: 16494 3.82 - 4.36: 17418 4.36 - 4.90: 30970 Nonbonded interactions: 76390 Sorted by model distance: nonbonded pdb=" O SER B 644 " pdb=" OG SER B 648 " model vdw 2.205 3.040 nonbonded pdb=" O SER B 601 " pdb=" OG SER B 601 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP B 444 " pdb=" N ARG B 445 " model vdw 2.251 3.120 nonbonded pdb=" NE2 GLN A 191 " pdb=" OD2 ASP A 295 " model vdw 2.259 3.120 nonbonded pdb=" OE1 GLU B 375 " pdb=" N LYS B 377 " model vdw 2.280 3.120 ... (remaining 76385 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 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 through 207 or (resid 208 and (name N or name CA or \ name C or name O or name CB )) or resid 209 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 224 or (resi \ d 225 and (name N or name CA or name C or name O or name CB )) or resid 226 thro \ ugh 246 or (resid 247 through 249 and (name N or name CA or name C or name O or \ name CB )) or resid 250 through 254 or (resid 255 through 256 and (name N or nam \ e CA or name C or name O or name CB )) or resid 257 through 351 or (resid 352 an \ d (name N or name CA or name C or name O or name CB )) or resid 353 through 407 \ or (resid 408 through 409 and (name N or name CA or name C or name O or name CB \ )) or resid 410 through 415 or (resid 416 through 417 and (name N or name CA or \ name C or name O or name CB )) or resid 418 through 462 or resid 464 through 483 \ or (resid 484 and (name N or name CA or name C or name O or name CB )) or resid \ 485 through 488 or (resid 491 through 492 and (name N or name CA or name C or n \ ame O or name CB )) or resid 493 through 503 or (resid 505 through 510 and (name \ N or name CA or name C or name O or name CB )) or resid 511 or (resid 512 throu \ gh 521 and (name N or name CA or name C or name O or name CB )) or resid 522 thr \ ough 524 or resid 528 through 538 or (resid 539 and (name N or name CA or name C \ or name O or name CB )) or resid 541 through 543 or (resid 550 through 556 and \ (name N or name CA or name C or name O or name CB )) or resid 557 through 558 or \ (resid 559 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 0 or (resid 561 through 563 and (name N or name CA or name C or name O or name C \ B )) or (resid 567 through 569 and (name N or name CA or name C or name O or nam \ e CB )) or resid 570 through 576 or (resid 577 and (name N or name CA or name C \ or name O or name CB )) or resid 578 through 593 or resid 595 or resid 597 throu \ gh 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) or \ resid 605 through 614 or (resid 615 and (name N or name CA or name C or name O \ or name CB )) or resid 616 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB )) or resid 620 through 630 or (resid 631 and (name N \ or name CA or name C or name O or name CB )) or resid 632 through 642 or (resid \ 643 and (name N or name CA or name C or name O or name CB )) or resid 644 throu \ gh 652 or (resid 653 through 654 and (name N or name CA or name C or name O or n \ ame CB )) or resid 655 through 658 or (resid 659 and (name N or name CA or name \ C or name O or name CB )) or resid 675 through 678 or (resid 679 and (name N or \ name CA or name C or name O or name CB )) or resid 680 through 681 or (resid 682 \ and (name N or name CA or name C or name O or name CB )) or resid 683 through 6 \ 90 or (resid 691 through 692 and (name N or name CA or name C or name O or name \ CB )) or resid 693 through 694 or (resid 695 through 697 and (name N or name CA \ or name C or name O or name CB )) or resid 698 through 705 or resid 709 through \ 712 or (resid 716 through 720 and (name N or name CA or name C or name O or name \ CB )) or resid 721 through 724 or (resid 725 through 729 and (name N or name CA \ or name C or name O or name CB )) or resid 730 or (resid 731 through 733 and (n \ ame N or name CA or name C or name O or name CB )) or resid 734 through 746 or ( \ resid 747 and (name N or name CA or name C or name O or name CB )) or resid 748 \ through 756 or (resid 757 through 762 and (name N or name CA or name C or name O \ or name CB )) or resid 763 through 775 or (resid 776 through 777 and (name N or \ name CA or name C or name O or name CB )) or resid 778 through 782 or (resid 78 \ 3 through 786 and (name N or name CA or name C or name O or name CB )) or resid \ 787 through 792 or (resid 793 through 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 through 799 or (resid 800 through 801 and (name \ N or name CA or name C or name O or name CB )) or resid 802 or (resid 803 throug \ h 806 and (name N or name CA or name C or name O or name CB )) or resid 807 or ( \ resid 808 through 811 and (name N or name CA or name C or name O or name CB )) o \ r resid 812 through 817 or (resid 818 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'B' and (resid 24 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 133 through 221 or (resid 222 through 223 a \ nd (name N or name CA or name C or name O or name CB )) or resid 224 through 238 \ or (resid 239 through 240 and (name N or name CA or name C or name O or name CB \ )) or resid 241 through 261 or (resid 262 through 264 and (name N or name CA or \ name C or name O or name CB )) or resid 265 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 2 \ 72 through 276 or (resid 277 and (name N or name CA or name C or name O or name \ CB )) or resid 278 through 282 or (resid 283 through 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 through 300 or (r \ esid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 t \ hrough 356 or (resid 357 through 361 and (name N or name CA or name C or name O \ or name CB )) or resid 362 through 365 or (resid 366 and (name N or name CA or n \ ame C or name O or name CB )) or resid 367 through 396 or (resid 397 through 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 4 \ 38 or (resid 439 through 440 and (name N or name CA or name C or name O or name \ CB )) or resid 441 through 489 or resid 492 through 499 or (resid 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 513 or (resi \ d 516 through 521 and (name N or name CA or name C or name O or name CB )) or re \ sid 522 through 524 or (resid 528 and (name N or name CA or name C or name O or \ name CB )) or resid 529 or resid 532 through 543 or (resid 550 through 551 and ( \ name N or name CA or name C or name O or name CB )) or resid 552 through 557 or \ (resid 558 through 559 and (name N or name CA or name C or name O or name CB )) \ or resid 560 through 562 or (resid 563 and (name N or name CA or name C or name \ O or name CB )) or (resid 567 through 569 and (name N or name CA or name C or na \ me O or name CB )) or resid 570 through 582 or (resid 583 through 584 and (name \ N or name CA or name C or name O or name CB )) or resid 585 through 597 or (resi \ d 598 and (name N or name CA or name C or name O or name CB )) or resid 599 thro \ ugh 606 or (resid 607 and (name N or name CA or name C or name O or name CB )) o \ r resid 608 or (resid 609 through 610 and (name N or name CA or name C or name O \ or name CB )) or resid 611 through 612 or (resid 613 through 615 and (name N or \ name CA or name C or name O or name CB )) or resid 616 through 620 or (resid 62 \ 1 through 623 and (name N or name CA or name C or name O or name CB )) or resid \ 624 through 632 or (resid 633 and (name N or name CA or name C or name O or name \ CB )) or resid 634 or (resid 635 through 637 and (name N or name CA or name C o \ r name O or name CB )) or resid 638 or (resid 639 and (name N or name CA or name \ C or name O or name CB )) or resid 640 or (resid 641 through 643 and (name N or \ name CA or name C or name O or name CB )) or resid 644 through 649 or (resid 65 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 651 through \ 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) or re \ sid 655 through 659 or resid 675 through 710 or (resid 711 through 720 and (name \ N or name CA or name C or name O or name CB )) or resid 721 through 735 or (res \ id 736 through 738 and (name N or name CA or name C or name O or name CB )) or r \ esid 739 or (resid 741 and (name N or name CA or name C or name O or name CB )) \ or resid 742 or (resid 743 and (name N or name CA or name C or name O or name CB \ )) or resid 744 or (resid 745 through 747 and (name N or name CA or name C or n \ ame O or name CB )) or resid 748 through 749 or (resid 750 through 751 and (name \ N or name CA or name C or name O or name CB )) or resid 752 through 753 or (res \ id 754 and (name N or name CA or name C or name O or name CB )) or resid 755 thr \ ough 759 or (resid 760 through 762 and (name N or name CA or name C or name O or \ name CB )) or (resid 763 through 768 and (name N or name CA or name C or name O \ or name CB )) or resid 769 or (resid 770 through 777 and (name N or name CA or \ name C or name O or name CB )) or resid 778 through 779 or (resid 780 through 78 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 787 or (resi \ d 788 and (name N or name CA or name C or name O or name CB )) or resid 789 thro \ ugh 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) o \ r resid 797 through 798 or (resid 799 through 801 and (name N or name CA or name \ C or name O or name CB )) or resid 802 through 815 or (resid 816 through 818 an \ d (name N or name CA or name C or name O or name CB )))) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 154.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.060 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.011 0.923 10612 Z= 0.728 Angle : 0.880 15.804 14534 Z= 0.544 Chirality : 0.055 0.392 1727 Planarity : 0.008 0.227 1880 Dihedral : 14.581 122.718 3451 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.56 % Allowed : 20.02 % Favored : 79.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1429 helix: 1.38 (0.20), residues: 694 sheet: -0.46 (0.41), residues: 164 loop : -1.14 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 487 HIS 0.004 0.001 HIS A 390 PHE 0.028 0.002 PHE B 201 TYR 0.022 0.002 TYR A 419 ARG 0.009 0.001 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 2) link_NAG-ASN : angle 2.05861 ( 6) hydrogen bonds : bond 0.15304 ( 547) hydrogen bonds : angle 5.67420 ( 1620) SS BOND : bond 0.00275 ( 10) SS BOND : angle 0.95134 ( 20) covalent geometry : bond 0.01093 (10600) covalent geometry : angle 0.87881 (14508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 1.049 Fit side-chains REVERT: A 349 TRP cc_start: 0.7908 (t-100) cc_final: 0.7617 (t60) REVERT: A 481 ASP cc_start: 0.7949 (p0) cc_final: 0.7662 (p0) REVERT: A 701 GLU cc_start: 0.8455 (tp30) cc_final: 0.7899 (pm20) REVERT: B 222 GLU cc_start: 0.7534 (mp0) cc_final: 0.7020 (mp0) REVERT: B 614 PHE cc_start: 0.7785 (t80) cc_final: 0.7498 (t80) REVERT: B 616 CYS cc_start: 0.8374 (m) cc_final: 0.7944 (m) REVERT: B 701 GLU cc_start: 0.7471 (tt0) cc_final: 0.6644 (tp30) outliers start: 5 outliers final: 2 residues processed: 207 average time/residue: 0.2738 time to fit residues: 80.2310 Evaluate side-chains 199 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 0.0070 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN B 73 ASN B 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121804 restraints weight = 19153.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124911 restraints weight = 10496.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126989 restraints weight = 6997.021| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10612 Z= 0.165 Angle : 0.540 5.599 14534 Z= 0.295 Chirality : 0.041 0.157 1727 Planarity : 0.004 0.058 1880 Dihedral : 8.484 126.571 1645 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.11 % Allowed : 16.13 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1431 helix: 1.62 (0.19), residues: 706 sheet: -0.15 (0.41), residues: 163 loop : -1.16 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 487 HIS 0.004 0.001 HIS A 390 PHE 0.025 0.002 PHE A 327 TYR 0.012 0.001 TYR A 165 ARG 0.006 0.001 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 1.75105 ( 6) hydrogen bonds : bond 0.05393 ( 547) hydrogen bonds : angle 4.54061 ( 1620) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.01465 ( 20) covalent geometry : bond 0.00366 (10600) covalent geometry : angle 0.53752 (14508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 2.604 Fit side-chains revert: symmetry clash REVERT: A 349 TRP cc_start: 0.8056 (t-100) cc_final: 0.7695 (t-100) REVERT: A 399 LEU cc_start: 0.8251 (tt) cc_final: 0.7999 (tt) REVERT: A 428 PHE cc_start: 0.8210 (p90) cc_final: 0.7818 (p90) REVERT: A 481 ASP cc_start: 0.7754 (p0) cc_final: 0.7549 (p0) REVERT: A 701 GLU cc_start: 0.7987 (tp30) cc_final: 0.7677 (tp30) REVERT: B 224 PHE cc_start: 0.8821 (t80) cc_final: 0.8562 (t80) REVERT: B 269 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 285 LEU cc_start: 0.8276 (mm) cc_final: 0.7967 (mp) REVERT: B 301 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: B 340 SER cc_start: 0.8644 (p) cc_final: 0.8339 (t) REVERT: B 473 TYR cc_start: 0.7928 (p90) cc_final: 0.7634 (p90) REVERT: B 701 GLU cc_start: 0.6649 (tt0) cc_final: 0.6096 (tp30) outliers start: 28 outliers final: 16 residues processed: 205 average time/residue: 0.2916 time to fit residues: 86.6768 Evaluate side-chains 210 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 191 GLN A 332 GLN A 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121438 restraints weight = 19715.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124605 restraints weight = 10965.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126685 restraints weight = 7317.922| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10612 Z= 0.149 Angle : 0.510 5.792 14534 Z= 0.278 Chirality : 0.041 0.191 1727 Planarity : 0.004 0.048 1880 Dihedral : 8.182 127.700 1643 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.67 % Allowed : 16.02 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1431 helix: 1.78 (0.20), residues: 699 sheet: -0.11 (0.41), residues: 163 loop : -1.17 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 474 HIS 0.003 0.001 HIS A 390 PHE 0.020 0.001 PHE A 327 TYR 0.011 0.001 TYR A 165 ARG 0.006 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 2) link_NAG-ASN : angle 1.76621 ( 6) hydrogen bonds : bond 0.04914 ( 547) hydrogen bonds : angle 4.31001 ( 1620) SS BOND : bond 0.00296 ( 10) SS BOND : angle 0.87616 ( 20) covalent geometry : bond 0.00327 (10600) covalent geometry : angle 0.50811 (14508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: A 367 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 395 MET cc_start: 0.7089 (tpt) cc_final: 0.6878 (tpp) REVERT: A 458 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8023 (t80) REVERT: A 701 GLU cc_start: 0.7959 (tp30) cc_final: 0.7654 (tp30) REVERT: B 94 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8268 (ttpt) REVERT: B 226 LEU cc_start: 0.8735 (tp) cc_final: 0.8480 (tt) REVERT: B 269 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 301 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: B 340 SER cc_start: 0.8645 (p) cc_final: 0.8362 (t) REVERT: B 473 TYR cc_start: 0.7930 (p90) cc_final: 0.7652 (p90) REVERT: B 608 ILE cc_start: 0.7650 (pt) cc_final: 0.7392 (mp) REVERT: B 614 PHE cc_start: 0.7378 (t80) cc_final: 0.7172 (t80) REVERT: B 701 GLU cc_start: 0.6498 (tt0) cc_final: 0.6050 (tp30) outliers start: 33 outliers final: 17 residues processed: 207 average time/residue: 0.3025 time to fit residues: 90.1328 Evaluate side-chains 211 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 191 GLN A 332 GLN A 390 HIS A 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119950 restraints weight = 19337.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123387 restraints weight = 10711.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125587 restraints weight = 7175.231| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10612 Z= 0.178 Angle : 0.526 6.210 14534 Z= 0.288 Chirality : 0.042 0.189 1727 Planarity : 0.004 0.087 1880 Dihedral : 8.188 127.883 1643 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.34 % Allowed : 17.13 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1431 helix: 1.69 (0.19), residues: 699 sheet: -0.14 (0.41), residues: 163 loop : -1.18 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.004 0.001 HIS A 390 PHE 0.023 0.002 PHE A 67 TYR 0.012 0.001 TYR B 453 ARG 0.005 0.000 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 1.88344 ( 6) hydrogen bonds : bond 0.05156 ( 547) hydrogen bonds : angle 4.31707 ( 1620) SS BOND : bond 0.00290 ( 10) SS BOND : angle 0.81644 ( 20) covalent geometry : bond 0.00398 (10600) covalent geometry : angle 0.52380 (14508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: A 395 MET cc_start: 0.6983 (tpt) cc_final: 0.6709 (tpp) REVERT: A 458 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 701 GLU cc_start: 0.8095 (tp30) cc_final: 0.7751 (tp30) REVERT: B 206 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 226 LEU cc_start: 0.8690 (tp) cc_final: 0.8463 (tt) REVERT: B 254 VAL cc_start: 0.8879 (m) cc_final: 0.8497 (p) REVERT: B 301 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 340 SER cc_start: 0.8673 (p) cc_final: 0.8398 (t) REVERT: B 473 TYR cc_start: 0.7963 (p90) cc_final: 0.7659 (p90) REVERT: B 608 ILE cc_start: 0.7794 (pt) cc_final: 0.7561 (mp) REVERT: B 614 PHE cc_start: 0.7555 (t80) cc_final: 0.7339 (t80) REVERT: B 701 GLU cc_start: 0.6819 (tt0) cc_final: 0.6172 (tp30) outliers start: 30 outliers final: 16 residues processed: 207 average time/residue: 0.3709 time to fit residues: 111.8672 Evaluate side-chains 211 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121513 restraints weight = 19467.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125016 restraints weight = 10653.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127225 restraints weight = 7150.015| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10612 Z= 0.155 Angle : 0.514 6.815 14534 Z= 0.279 Chirality : 0.041 0.194 1727 Planarity : 0.004 0.076 1880 Dihedral : 8.086 128.236 1643 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.67 % Allowed : 17.58 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1431 helix: 1.78 (0.20), residues: 699 sheet: 0.10 (0.41), residues: 167 loop : -1.20 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 349 HIS 0.004 0.001 HIS A 390 PHE 0.021 0.001 PHE A 67 TYR 0.010 0.001 TYR B 453 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 1.84908 ( 6) hydrogen bonds : bond 0.04850 ( 547) hydrogen bonds : angle 4.21019 ( 1620) SS BOND : bond 0.00257 ( 10) SS BOND : angle 0.77002 ( 20) covalent geometry : bond 0.00344 (10600) covalent geometry : angle 0.51245 (14508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: A 395 MET cc_start: 0.7112 (tpt) cc_final: 0.6817 (tpp) REVERT: A 399 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 458 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (t80) REVERT: B 206 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 226 LEU cc_start: 0.8728 (tp) cc_final: 0.8487 (tt) REVERT: B 254 VAL cc_start: 0.8878 (m) cc_final: 0.8517 (p) REVERT: B 269 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 301 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 340 SER cc_start: 0.8677 (p) cc_final: 0.8397 (t) REVERT: B 473 TYR cc_start: 0.7948 (p90) cc_final: 0.7623 (p90) REVERT: B 701 GLU cc_start: 0.6731 (tt0) cc_final: 0.6115 (tp30) outliers start: 33 outliers final: 17 residues processed: 217 average time/residue: 0.2777 time to fit residues: 86.0171 Evaluate side-chains 217 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 0.0170 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN A 414 ASN A 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118068 restraints weight = 19783.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121524 restraints weight = 10842.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123668 restraints weight = 7258.193| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10612 Z= 0.149 Angle : 0.513 5.776 14534 Z= 0.279 Chirality : 0.041 0.202 1727 Planarity : 0.004 0.067 1880 Dihedral : 8.026 128.328 1643 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.45 % Allowed : 18.91 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1431 helix: 1.80 (0.20), residues: 699 sheet: 0.09 (0.41), residues: 167 loop : -1.21 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 349 HIS 0.004 0.001 HIS A 390 PHE 0.020 0.001 PHE A 67 TYR 0.010 0.001 TYR B 322 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 2) link_NAG-ASN : angle 1.78647 ( 6) hydrogen bonds : bond 0.04726 ( 547) hydrogen bonds : angle 4.14995 ( 1620) SS BOND : bond 0.00265 ( 10) SS BOND : angle 0.77797 ( 20) covalent geometry : bond 0.00332 (10600) covalent geometry : angle 0.51164 (14508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 185 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (t) REVERT: A 399 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 458 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 206 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6991 (t80) REVERT: B 226 LEU cc_start: 0.8740 (tp) cc_final: 0.8503 (tt) REVERT: B 254 VAL cc_start: 0.8861 (m) cc_final: 0.8506 (p) REVERT: B 269 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 301 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7406 (mm-30) REVERT: B 340 SER cc_start: 0.8673 (p) cc_final: 0.8403 (t) REVERT: B 396 HIS cc_start: 0.7547 (t70) cc_final: 0.7311 (t70) REVERT: B 473 TYR cc_start: 0.7924 (p90) cc_final: 0.7634 (p90) REVERT: B 608 ILE cc_start: 0.7742 (pt) cc_final: 0.7518 (mp) REVERT: B 614 PHE cc_start: 0.7440 (t80) cc_final: 0.7149 (t80) REVERT: B 618 CYS cc_start: 0.7708 (m) cc_final: 0.7471 (m) REVERT: B 701 GLU cc_start: 0.6675 (tt0) cc_final: 0.6039 (tp30) outliers start: 31 outliers final: 19 residues processed: 212 average time/residue: 0.2371 time to fit residues: 70.7576 Evaluate side-chains 212 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 0.0070 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.148584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122249 restraints weight = 19974.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125809 restraints weight = 10754.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128084 restraints weight = 7141.236| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10612 Z= 0.131 Angle : 0.508 6.004 14534 Z= 0.275 Chirality : 0.040 0.203 1727 Planarity : 0.004 0.063 1880 Dihedral : 7.907 128.628 1643 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.34 % Allowed : 19.35 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1431 helix: 1.90 (0.20), residues: 694 sheet: 0.14 (0.41), residues: 167 loop : -1.20 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.002 0.001 HIS A 87 PHE 0.018 0.001 PHE A 67 TYR 0.009 0.001 TYR B 458 ARG 0.008 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 2) link_NAG-ASN : angle 1.73443 ( 6) hydrogen bonds : bond 0.04422 ( 547) hydrogen bonds : angle 4.04386 ( 1620) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.73620 ( 20) covalent geometry : bond 0.00292 (10600) covalent geometry : angle 0.50656 (14508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: A 185 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8347 (t) REVERT: A 349 TRP cc_start: 0.8128 (t-100) cc_final: 0.7693 (t-100) REVERT: A 399 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 416 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7618 (ttp80) REVERT: A 458 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8072 (t80) REVERT: B 206 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 226 LEU cc_start: 0.8770 (tp) cc_final: 0.8532 (tt) REVERT: B 254 VAL cc_start: 0.8814 (m) cc_final: 0.8463 (p) REVERT: B 269 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: B 301 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 340 SER cc_start: 0.8667 (p) cc_final: 0.8392 (t) REVERT: B 473 TYR cc_start: 0.7899 (p90) cc_final: 0.7608 (p90) REVERT: B 608 ILE cc_start: 0.7634 (pt) cc_final: 0.7402 (mp) REVERT: B 701 GLU cc_start: 0.6483 (tt0) cc_final: 0.5938 (tp30) outliers start: 30 outliers final: 19 residues processed: 209 average time/residue: 0.2413 time to fit residues: 71.8803 Evaluate side-chains 214 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119397 restraints weight = 19626.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122854 restraints weight = 10742.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125119 restraints weight = 7208.525| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10612 Z= 0.236 Angle : 0.590 5.651 14534 Z= 0.323 Chirality : 0.044 0.230 1727 Planarity : 0.004 0.067 1880 Dihedral : 8.286 128.594 1643 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.67 % Allowed : 20.47 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1431 helix: 1.56 (0.20), residues: 693 sheet: -0.13 (0.41), residues: 167 loop : -1.39 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 349 HIS 0.004 0.001 HIS B 87 PHE 0.028 0.002 PHE B 67 TYR 0.015 0.002 TYR B 453 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 2) link_NAG-ASN : angle 2.01413 ( 6) hydrogen bonds : bond 0.05569 ( 547) hydrogen bonds : angle 4.38724 ( 1620) SS BOND : bond 0.00326 ( 10) SS BOND : angle 1.42094 ( 20) covalent geometry : bond 0.00532 (10600) covalent geometry : angle 0.58673 (14508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 416 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7639 (ttp80) REVERT: B 206 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 226 LEU cc_start: 0.8729 (tp) cc_final: 0.8514 (tt) REVERT: B 254 VAL cc_start: 0.8864 (m) cc_final: 0.8533 (p) REVERT: B 301 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7412 (mm-30) REVERT: B 340 SER cc_start: 0.8685 (p) cc_final: 0.8407 (t) REVERT: B 473 TYR cc_start: 0.7968 (p90) cc_final: 0.7654 (p90) REVERT: B 608 ILE cc_start: 0.7883 (pt) cc_final: 0.7661 (mp) REVERT: B 701 GLU cc_start: 0.6744 (tt0) cc_final: 0.6011 (tp30) outliers start: 24 outliers final: 17 residues processed: 206 average time/residue: 0.2316 time to fit residues: 67.2367 Evaluate side-chains 204 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120403 restraints weight = 19910.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123619 restraints weight = 10961.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125710 restraints weight = 7389.062| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10612 Z= 0.189 Angle : 0.559 5.982 14534 Z= 0.304 Chirality : 0.042 0.203 1727 Planarity : 0.004 0.061 1880 Dihedral : 8.268 129.446 1643 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.56 % Allowed : 20.24 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1431 helix: 1.62 (0.20), residues: 692 sheet: -0.13 (0.42), residues: 160 loop : -1.36 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 349 HIS 0.004 0.001 HIS B 365 PHE 0.023 0.002 PHE A 67 TYR 0.018 0.001 TYR B 322 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 1.93900 ( 6) hydrogen bonds : bond 0.05099 ( 547) hydrogen bonds : angle 4.26337 ( 1620) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.04268 ( 20) covalent geometry : bond 0.00426 (10600) covalent geometry : angle 0.55702 (14508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 185 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8320 (t) REVERT: A 349 TRP cc_start: 0.8153 (t-100) cc_final: 0.7822 (t-100) REVERT: A 399 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 414 ASN cc_start: 0.7784 (t0) cc_final: 0.7476 (t0) REVERT: A 416 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7569 (ttp80) REVERT: B 226 LEU cc_start: 0.8772 (tp) cc_final: 0.8537 (tt) REVERT: B 254 VAL cc_start: 0.8856 (m) cc_final: 0.8514 (p) REVERT: B 301 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 340 SER cc_start: 0.8657 (p) cc_final: 0.8390 (t) REVERT: B 458 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7409 (t80) REVERT: B 473 TYR cc_start: 0.7924 (p90) cc_final: 0.7646 (p90) REVERT: B 608 ILE cc_start: 0.7760 (pt) cc_final: 0.7558 (mp) outliers start: 23 outliers final: 16 residues processed: 204 average time/residue: 0.2278 time to fit residues: 64.8169 Evaluate side-chains 204 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 106 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 129 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121588 restraints weight = 19610.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125144 restraints weight = 10622.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127438 restraints weight = 7067.267| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10612 Z= 0.137 Angle : 0.549 6.848 14534 Z= 0.296 Chirality : 0.041 0.245 1727 Planarity : 0.004 0.067 1880 Dihedral : 8.099 129.436 1643 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.89 % Allowed : 21.47 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1431 helix: 1.84 (0.20), residues: 691 sheet: -0.01 (0.42), residues: 160 loop : -1.36 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 349 HIS 0.002 0.001 HIS B 87 PHE 0.018 0.001 PHE A 67 TYR 0.012 0.001 TYR B 458 ARG 0.008 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 1.77202 ( 6) hydrogen bonds : bond 0.04532 ( 547) hydrogen bonds : angle 4.10000 ( 1620) SS BOND : bond 0.00249 ( 10) SS BOND : angle 0.95798 ( 20) covalent geometry : bond 0.00304 (10600) covalent geometry : angle 0.54666 (14508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 185 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 349 TRP cc_start: 0.8080 (t-100) cc_final: 0.7661 (t-100) REVERT: A 416 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7589 (ttp80) REVERT: A 619 MET cc_start: 0.6824 (tpt) cc_final: 0.6569 (tpt) REVERT: B 172 LEU cc_start: 0.8948 (mt) cc_final: 0.8729 (mp) REVERT: B 226 LEU cc_start: 0.8707 (tp) cc_final: 0.8497 (tt) REVERT: B 254 VAL cc_start: 0.8863 (m) cc_final: 0.8517 (p) REVERT: B 301 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 340 SER cc_start: 0.8669 (p) cc_final: 0.8403 (t) REVERT: B 458 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 473 TYR cc_start: 0.7931 (p90) cc_final: 0.7630 (p90) REVERT: B 608 ILE cc_start: 0.7666 (pt) cc_final: 0.7458 (mp) outliers start: 17 outliers final: 15 residues processed: 200 average time/residue: 0.2246 time to fit residues: 63.7201 Evaluate side-chains 206 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 7.9990 chunk 100 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 134 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.147980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121816 restraints weight = 19595.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125285 restraints weight = 10621.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127576 restraints weight = 7114.527| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10612 Z= 0.135 Angle : 0.536 6.105 14534 Z= 0.289 Chirality : 0.041 0.207 1727 Planarity : 0.004 0.059 1880 Dihedral : 7.985 129.089 1643 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.11 % Allowed : 21.25 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1431 helix: 1.89 (0.20), residues: 692 sheet: 0.00 (0.41), residues: 160 loop : -1.31 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.002 0.001 HIS A 87 PHE 0.018 0.001 PHE A 67 TYR 0.013 0.001 TYR A 180 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 2) link_NAG-ASN : angle 1.68593 ( 6) hydrogen bonds : bond 0.04406 ( 547) hydrogen bonds : angle 4.02695 ( 1620) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.88784 ( 20) covalent geometry : bond 0.00300 (10600) covalent geometry : angle 0.53454 (14508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4333.46 seconds wall clock time: 80 minutes 51.76 seconds (4851.76 seconds total)