Starting phenix.real_space_refine on Sun Apr 5 17:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.map" model { file = "/net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9llz_63210/04_2026/9llz_63210.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 76 5.16 5 C 7617 2.51 5 N 2060 2.21 5 O 2225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5977 Classifications: {'peptide': 779} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 735} Chain breaks: 3 Chain: "A" Number of atoms: 5981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5981 Classifications: {'peptide': 779} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 734} Chain breaks: 3 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.23 Number of scatterers: 11980 At special positions: 0 Unit cell: (96.672, 98.368, 184.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 2 15.00 O 2225 8.00 N 2060 7.00 C 7617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.04 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 744 " 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 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 593.0 milliseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2876 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 47.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.572A pdb=" N VAL B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.887A pdb=" N MET B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.789A pdb=" N VAL B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.622A pdb=" N LEU B 181 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 4.339A pdb=" N GLN B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.591A pdb=" N ILE B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 337 through 345 removed outlier: 3.539A pdb=" N GLN B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 400 through 423 removed outlier: 3.610A pdb=" N VAL B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 446 removed outlier: 3.714A pdb=" N GLN B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.912A pdb=" N TYR B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 620 removed outlier: 3.843A pdb=" N SER B 619 " --> pdb=" O ILE B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 642 removed outlier: 4.349A pdb=" N THR B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 680 removed outlier: 3.831A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 719 removed outlier: 3.536A pdb=" N GLN B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 772 removed outlier: 5.242A pdb=" N TYR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER B 758 " --> pdb=" O CYS B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 806 removed outlier: 3.744A pdb=" N ILE B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Proline residue: B 801 - end of helix Processing helix chain 'B' and resid 812 through 836 removed outlier: 4.106A pdb=" N THR B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B 818 " --> pdb=" O TYR B 814 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 822 " --> pdb=" O THR B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 846 Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.718A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.801A pdb=" N MET A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.731A pdb=" N SER A 182 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.849A pdb=" N ARG A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.689A pdb=" N THR A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.599A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.581A pdb=" N VAL A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.697A pdb=" N GLN A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.552A pdb=" N ALA A 503 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 610 Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.576A pdb=" N SER A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 3.741A pdb=" N SER A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 639 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 680 removed outlier: 3.826A pdb=" N ARG A 654 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 719 removed outlier: 3.780A pdb=" N GLN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 719 " --> pdb=" O TRP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 772 removed outlier: 4.989A pdb=" N TYR A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER A 758 " --> pdb=" O CYS A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 806 removed outlier: 3.682A pdb=" N GLY A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 800 " --> pdb=" O TRP A 796 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 812 through 836 removed outlier: 3.751A pdb=" N GLN A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR A 818 " --> pdb=" O TYR A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.999A pdb=" N ALA B 93 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 41 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 40 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 147 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE B 172 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 148 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 251 removed outlier: 7.951A pdb=" N VAL B 216 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER B 248 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B 218 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS B 250 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 220 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY B 275 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 276 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.980A pdb=" N ILE B 472 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 491 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN B 474 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ALA B 489 " --> pdb=" O GLN B 474 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B 476 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR B 487 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR B 478 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 485 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 450 through 451 removed outlier: 3.571A pdb=" N PHE B 450 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AA6, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AA7, first strand: chain 'B' and resid 724 through 726 Processing sheet with id=AA8, first strand: chain 'A' and resid 33 through 34 removed outlier: 7.341A pdb=" N LEU A 41 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 40 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 147 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 149 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ILE A 172 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 148 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN A 171 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 244 through 251 removed outlier: 7.844A pdb=" N VAL A 216 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER A 248 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR A 218 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS A 250 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 220 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 275 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 491 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 474 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA A 489 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 450 through 451 removed outlier: 3.758A pdb=" N PHE A 450 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 531 removed outlier: 3.776A pdb=" N VAL A 531 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS A 537 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 547 through 549 Processing sheet with id=AB4, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AB5, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.633A pdb=" N VAL A 741 " --> pdb=" O ASP A 726 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3927 1.35 - 1.46: 2848 1.46 - 1.58: 5359 1.58 - 1.70: 2 1.70 - 1.82: 110 Bond restraints: 12246 Sorted by residual: bond pdb=" O1P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O2P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O2P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O3P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O1P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 12241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 16348 1.53 - 3.06: 245 3.06 - 4.58: 45 4.58 - 6.11: 16 6.11 - 7.64: 4 Bond angle restraints: 16658 Sorted by residual: angle pdb=" N LEU A 663 " pdb=" CA LEU A 663 " pdb=" C LEU A 663 " ideal model delta sigma weight residual 111.07 114.23 -3.16 1.07e+00 8.73e-01 8.70e+00 angle pdb=" CB SEP A1001 " pdb=" OG SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 110.00 117.64 -7.64 3.00e+00 1.11e-01 6.49e+00 angle pdb=" CA PRO B 735 " pdb=" N PRO B 735 " pdb=" CD PRO B 735 " ideal model delta sigma weight residual 112.00 108.50 3.50 1.40e+00 5.10e-01 6.24e+00 angle pdb=" CB SEP B1001 " pdb=" OG SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 110.00 116.91 -6.91 3.00e+00 1.11e-01 5.31e+00 angle pdb=" C GLY A 833 " pdb=" N MET A 834 " pdb=" CA MET A 834 " ideal model delta sigma weight residual 122.09 118.25 3.84 1.79e+00 3.12e-01 4.60e+00 ... (remaining 16653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6621 17.91 - 35.82: 606 35.82 - 53.73: 103 53.73 - 71.63: 5 71.63 - 89.54: 10 Dihedral angle restraints: 7345 sinusoidal: 2865 harmonic: 4480 Sorted by residual: dihedral pdb=" CB CYS B 650 " pdb=" SG CYS B 650 " pdb=" SG CYS B 744 " pdb=" CB CYS B 744 " ideal model delta sinusoidal sigma weight residual 93.00 -179.92 -87.08 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A 423 " pdb=" SG CYS A 423 " pdb=" SG CYS A 430 " pdb=" CB CYS A 430 " ideal model delta sinusoidal sigma weight residual 93.00 179.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS B 558 " pdb=" SG CYS B 558 " pdb=" SG CYS B 571 " pdb=" CB CYS B 571 " ideal model delta sinusoidal sigma weight residual 93.00 173.03 -80.03 1 1.00e+01 1.00e-02 7.94e+01 ... (remaining 7342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1091 0.027 - 0.054: 484 0.054 - 0.081: 202 0.081 - 0.108: 97 0.108 - 0.134: 26 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ILE B 277 " pdb=" N ILE B 277 " pdb=" C ILE B 277 " pdb=" CB ILE B 277 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 725 " pdb=" N ILE B 725 " pdb=" C ILE B 725 " pdb=" CB ILE B 725 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1897 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 734 " 0.037 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO B 735 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 735 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 735 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 734 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 735 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 735 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 735 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 330 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 331 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " -0.023 5.00e-02 4.00e+02 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1231 2.75 - 3.29: 11393 3.29 - 3.82: 18691 3.82 - 4.36: 21118 4.36 - 4.90: 38732 Nonbonded interactions: 91165 Sorted by model distance: nonbonded pdb=" O ILE B 802 " pdb=" OG1 THR B 806 " model vdw 2.211 3.040 nonbonded pdb=" NH2 ARG A 274 " pdb=" OD1 ASP A 509 " model vdw 2.229 3.120 nonbonded pdb=" O TYR A 215 " pdb=" OG SER A 516 " model vdw 2.254 3.040 nonbonded pdb=" N GLU A 728 " pdb=" OE1 GLU A 728 " model vdw 2.287 3.120 nonbonded pdb=" O THR B 806 " pdb=" OG SER B 809 " model vdw 2.297 3.040 ... (remaining 91160 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 29 through 680 or resid 692 through 1001)) selection = (chain 'B' and (resid 29 through 371 or resid 378 through 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.540 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.003 0.102 12263 Z= 0.157 Angle : 0.516 7.641 16692 Z= 0.261 Chirality : 0.040 0.134 1900 Planarity : 0.004 0.055 2138 Dihedral : 13.328 89.542 4418 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1542 helix: 1.54 (0.20), residues: 679 sheet: -1.67 (0.38), residues: 179 loop : -1.28 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.014 0.001 TYR A 665 PHE 0.010 0.001 PHE A 260 TRP 0.012 0.001 TRP A 715 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00325 (12246) covalent geometry : angle 0.51539 (16658) SS BOND : bond 0.00188 ( 17) SS BOND : angle 0.89464 ( 34) hydrogen bonds : bond 0.15233 ( 548) hydrogen bonds : angle 5.77088 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.438 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1027 time to fit residues: 19.4741 Evaluate side-chains 111 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.190289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154064 restraints weight = 13648.773| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.44 r_work: 0.3261 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12263 Z= 0.118 Angle : 0.502 7.869 16692 Z= 0.257 Chirality : 0.040 0.137 1900 Planarity : 0.004 0.042 2138 Dihedral : 4.010 34.356 1710 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.86 % Allowed : 4.37 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1542 helix: 1.62 (0.20), residues: 691 sheet: -1.35 (0.39), residues: 182 loop : -1.30 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.010 0.001 TYR A 665 PHE 0.011 0.001 PHE A 260 TRP 0.009 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00265 (12246) covalent geometry : angle 0.50097 (16658) SS BOND : bond 0.00267 ( 17) SS BOND : angle 0.94259 ( 34) hydrogen bonds : bond 0.04199 ( 548) hydrogen bonds : angle 4.17615 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 420 GLN cc_start: 0.7787 (mm110) cc_final: 0.7333 (tm-30) REVERT: B 495 GLU cc_start: 0.8573 (tp30) cc_final: 0.8199 (tt0) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1052 time to fit residues: 18.3420 Evaluate side-chains 116 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 832 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.189827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156453 restraints weight = 13809.719| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.43 r_work: 0.3280 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12263 Z= 0.117 Angle : 0.486 7.481 16692 Z= 0.247 Chirality : 0.040 0.136 1900 Planarity : 0.004 0.047 2138 Dihedral : 3.972 33.722 1710 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.17 % Allowed : 6.16 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1542 helix: 1.68 (0.20), residues: 692 sheet: -1.18 (0.39), residues: 182 loop : -1.28 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.010 0.001 TYR A 665 PHE 0.010 0.001 PHE A 260 TRP 0.011 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00267 (12246) covalent geometry : angle 0.48559 (16658) SS BOND : bond 0.00226 ( 17) SS BOND : angle 0.80342 ( 34) hydrogen bonds : bond 0.03902 ( 548) hydrogen bonds : angle 3.90637 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8489 (mm-30) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.1055 time to fit residues: 17.9354 Evaluate side-chains 112 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 832 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150021 restraints weight = 13711.912| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.42 r_work: 0.3202 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12263 Z= 0.197 Angle : 0.541 7.108 16692 Z= 0.277 Chirality : 0.042 0.138 1900 Planarity : 0.004 0.051 2138 Dihedral : 4.270 34.293 1710 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.09 % Allowed : 9.28 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1542 helix: 1.43 (0.20), residues: 703 sheet: -1.20 (0.38), residues: 182 loop : -1.38 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.011 0.001 TYR A 475 PHE 0.012 0.001 PHE B 279 TRP 0.018 0.001 TRP A 303 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00485 (12246) covalent geometry : angle 0.53941 (16658) SS BOND : bond 0.00283 ( 17) SS BOND : angle 1.03146 ( 34) hydrogen bonds : bond 0.04566 ( 548) hydrogen bonds : angle 3.92088 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8454 (mm-30) REVERT: B 495 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8284 (tt0) REVERT: B 812 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7885 (mmtp) outliers start: 14 outliers final: 10 residues processed: 116 average time/residue: 0.1036 time to fit residues: 17.7497 Evaluate side-chains 113 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.188962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153455 restraints weight = 13734.564| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.47 r_work: 0.3238 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12263 Z= 0.120 Angle : 0.489 7.013 16692 Z= 0.248 Chirality : 0.040 0.133 1900 Planarity : 0.004 0.052 2138 Dihedral : 4.068 34.222 1710 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.40 % Allowed : 10.37 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1542 helix: 1.61 (0.20), residues: 698 sheet: -1.10 (0.38), residues: 182 loop : -1.27 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.009 0.001 TYR A 665 PHE 0.011 0.001 PHE A 260 TRP 0.012 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00280 (12246) covalent geometry : angle 0.48789 (16658) SS BOND : bond 0.00221 ( 17) SS BOND : angle 0.78043 ( 34) hydrogen bonds : bond 0.03784 ( 548) hydrogen bonds : angle 3.76374 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 495 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8334 (tt0) REVERT: B 812 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7841 (mmtp) outliers start: 18 outliers final: 13 residues processed: 119 average time/residue: 0.1085 time to fit residues: 19.1777 Evaluate side-chains 121 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152423 restraints weight = 13775.724| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.35 r_work: 0.3243 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12263 Z= 0.136 Angle : 0.495 6.974 16692 Z= 0.251 Chirality : 0.041 0.134 1900 Planarity : 0.004 0.053 2138 Dihedral : 4.075 33.555 1710 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.40 % Allowed : 11.23 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1542 helix: 1.60 (0.20), residues: 698 sheet: -1.04 (0.38), residues: 182 loop : -1.27 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.009 0.001 TYR A 665 PHE 0.011 0.001 PHE A 260 TRP 0.014 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00324 (12246) covalent geometry : angle 0.49421 (16658) SS BOND : bond 0.00237 ( 17) SS BOND : angle 0.82759 ( 34) hydrogen bonds : bond 0.03876 ( 548) hydrogen bonds : angle 3.73129 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8366 (mm-30) REVERT: B 420 GLN cc_start: 0.7748 (mm110) cc_final: 0.7229 (tm-30) REVERT: B 495 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8466 (tp30) outliers start: 18 outliers final: 16 residues processed: 118 average time/residue: 0.1031 time to fit residues: 18.1575 Evaluate side-chains 122 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 746 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 835 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 0.0170 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 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.189878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154094 restraints weight = 13669.589| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.40 r_work: 0.3260 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12263 Z= 0.108 Angle : 0.477 6.933 16692 Z= 0.242 Chirality : 0.040 0.133 1900 Planarity : 0.004 0.053 2138 Dihedral : 3.945 33.149 1710 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.48 % Allowed : 11.93 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1542 helix: 1.69 (0.20), residues: 698 sheet: -0.96 (0.39), residues: 182 loop : -1.21 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.009 0.001 TYR A 665 PHE 0.010 0.001 PHE A 260 TRP 0.010 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00248 (12246) covalent geometry : angle 0.47637 (16658) SS BOND : bond 0.00202 ( 17) SS BOND : angle 0.72310 ( 34) hydrogen bonds : bond 0.03520 ( 548) hydrogen bonds : angle 3.64797 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 GLN cc_start: 0.7750 (mm110) cc_final: 0.7229 (tm-30) REVERT: B 495 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8464 (tp30) REVERT: A 789 MET cc_start: 0.8598 (mmp) cc_final: 0.8372 (mmp) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1094 time to fit residues: 19.6164 Evaluate side-chains 124 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 835 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 0.0030 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 66 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155011 restraints weight = 13642.748| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.43 r_work: 0.3263 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12263 Z= 0.099 Angle : 0.485 8.725 16692 Z= 0.243 Chirality : 0.040 0.130 1900 Planarity : 0.004 0.053 2138 Dihedral : 3.849 32.105 1710 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.33 % Allowed : 12.17 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1542 helix: 1.74 (0.20), residues: 699 sheet: -0.90 (0.38), residues: 184 loop : -1.14 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 352 TYR 0.013 0.001 TYR B 665 PHE 0.010 0.001 PHE A 260 TRP 0.009 0.001 TRP A 303 HIS 0.001 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00220 (12246) covalent geometry : angle 0.48489 (16658) SS BOND : bond 0.00202 ( 17) SS BOND : angle 0.68766 ( 34) hydrogen bonds : bond 0.03348 ( 548) hydrogen bonds : angle 3.60255 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 GLN cc_start: 0.7774 (mm110) cc_final: 0.7232 (tm-30) REVERT: B 495 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8469 (tp30) REVERT: A 789 MET cc_start: 0.8623 (mmp) cc_final: 0.8087 (mmp) outliers start: 17 outliers final: 15 residues processed: 115 average time/residue: 0.1008 time to fit residues: 17.3404 Evaluate side-chains 120 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 0.0020 chunk 42 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.188865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153264 restraints weight = 13746.023| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.39 r_work: 0.3236 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12263 Z= 0.149 Angle : 0.525 15.985 16692 Z= 0.263 Chirality : 0.041 0.176 1900 Planarity : 0.004 0.053 2138 Dihedral : 4.019 32.405 1710 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.64 % Allowed : 12.17 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1542 helix: 1.64 (0.20), residues: 700 sheet: -0.89 (0.39), residues: 182 loop : -1.21 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.015 0.001 TYR B 665 PHE 0.009 0.001 PHE B 279 TRP 0.015 0.001 TRP A 303 HIS 0.002 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00363 (12246) covalent geometry : angle 0.52416 (16658) SS BOND : bond 0.00235 ( 17) SS BOND : angle 0.84425 ( 34) hydrogen bonds : bond 0.03881 ( 548) hydrogen bonds : angle 3.67863 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 495 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8521 (tp30) REVERT: A 789 MET cc_start: 0.8616 (mmp) cc_final: 0.8100 (mmp) outliers start: 21 outliers final: 19 residues processed: 117 average time/residue: 0.0962 time to fit residues: 17.0059 Evaluate side-chains 123 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 0.9990 chunk 115 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153963 restraints weight = 13744.699| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.39 r_work: 0.3254 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12263 Z= 0.119 Angle : 0.516 16.686 16692 Z= 0.256 Chirality : 0.041 0.218 1900 Planarity : 0.004 0.053 2138 Dihedral : 3.954 32.683 1710 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.48 % Allowed : 12.71 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1542 helix: 1.66 (0.20), residues: 699 sheet: -0.89 (0.38), residues: 182 loop : -1.18 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 352 TYR 0.010 0.001 TYR B 665 PHE 0.010 0.001 PHE A 260 TRP 0.012 0.001 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00278 (12246) covalent geometry : angle 0.51555 (16658) SS BOND : bond 0.00212 ( 17) SS BOND : angle 0.75700 ( 34) hydrogen bonds : bond 0.03633 ( 548) hydrogen bonds : angle 3.65702 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 GLN cc_start: 0.7738 (mm110) cc_final: 0.7223 (tm-30) REVERT: B 495 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8534 (tp30) REVERT: B 834 MET cc_start: 0.7497 (tmm) cc_final: 0.7258 (tmm) REVERT: A 789 MET cc_start: 0.8638 (mmp) cc_final: 0.8153 (mmp) outliers start: 19 outliers final: 17 residues processed: 114 average time/residue: 0.0972 time to fit residues: 16.7235 Evaluate side-chains 121 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 0.0970 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.187166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151283 restraints weight = 13745.466| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.38 r_work: 0.3228 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12263 Z= 0.174 Angle : 0.543 14.295 16692 Z= 0.273 Chirality : 0.042 0.220 1900 Planarity : 0.004 0.053 2138 Dihedral : 4.130 33.059 1710 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.48 % Allowed : 12.87 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1542 helix: 1.49 (0.20), residues: 705 sheet: -0.93 (0.38), residues: 182 loop : -1.30 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 352 TYR 0.011 0.001 TYR B 665 PHE 0.011 0.001 PHE B 279 TRP 0.017 0.001 TRP A 303 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00427 (12246) covalent geometry : angle 0.54174 (16658) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.91239 ( 34) hydrogen bonds : bond 0.04172 ( 548) hydrogen bonds : angle 3.74742 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.62 seconds wall clock time: 55 minutes 41.64 seconds (3341.64 seconds total)