Starting phenix.real_space_refine on Fri Jan 19 04:34:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_23994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_23994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_23994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_23994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/01_2024/7mtq_23994_updated.pdb" } 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 Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 6.38, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.43 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 47.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 55 through 73 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 95 through 109 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 145 through 158 removed outlier: 4.399A pdb=" N LEU A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.821A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 376 through 399 removed outlier: 4.337A pdb=" N MET A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 399 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 566 through 593 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 596 through 599 No H-bonds generated for 'chain 'A' and resid 596 through 599' Processing helix chain 'A' and resid 604 through 623 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) Processing helix chain 'A' and resid 629 through 658 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) Processing helix chain 'A' and resid 676 through 700 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) Processing helix chain 'A' and resid 725 through 751 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) removed outlier: 5.015A pdb=" N LEU A 741 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N CYS A 742 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR A 743 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 744 " --> pdb=" O ILE A 739 " (cutoff:3.500A) 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) removed outlier: 4.407A pdb=" N LYS A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 783 removed outlier: 3.522A pdb=" N GLU A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA A 759 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Proline residue: A 778 - end of helix removed outlier: 3.549A pdb=" N THR A 783 " --> pdb=" O PHE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 817 Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 95 through 109 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 145 through 158 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 170 through 173 removed outlier: 3.834A pdb=" N SER B 173 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.518A pdb=" N PHE B 201 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.510A pdb=" N GLY B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.920A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 376 through 399 removed outlier: 4.513A pdb=" N MET B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 380 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 399 " --> pdb=" O HIS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 568 through 591 Processing helix chain 'B' and resid 605 through 623 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) Processing helix chain 'B' and resid 629 through 656 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 676 through 700 removed outlier: 3.899A pdb=" N VAL B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 748 Processing helix chain 'B' and resid 758 through 785 Proline residue: B 778 - end of helix removed outlier: 4.913A pdb=" N SER B 785 " --> pdb=" O TYR B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 818 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= A, 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: 6.435A pdb=" N GLY A 138 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 37 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 140 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLY A 141 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE A 163 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 238 through 241 removed outlier: 6.633A pdb=" N THR A 209 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A 241 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 211 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 290 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 268 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 292 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 315 through 319 removed outlier: 3.537A pdb=" N ILE A 455 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= D, 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: 7.145A pdb=" N GLY B 35 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 139 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B 37 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY B 141 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 141 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE B 163 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.456A pdb=" N THR B 290 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 268 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 292 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.731A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1251 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: 3.27 Time building geometry restraints manager: 4.74 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: 59.97 - 75.01: 6 75.01 - 90.05: 0 90.05 - 105.10: 218 105.10 - 120.14: 9500 120.14 - 135.19: 4784 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: 1331 2.74 - 3.28: 10247 3.28 - 3.82: 16495 3.82 - 4.36: 17539 4.36 - 4.90: 30994 Nonbonded interactions: 76606 Sorted by model distance: nonbonded pdb=" O SER B 644 " pdb=" OG SER B 648 " model vdw 2.205 2.440 nonbonded pdb=" O SER B 601 " pdb=" OG SER B 601 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASP B 444 " pdb=" N ARG B 445 " model vdw 2.251 2.520 nonbonded pdb=" NE2 GLN A 191 " pdb=" OD2 ASP A 295 " model vdw 2.259 2.520 nonbonded pdb=" OE1 GLU B 375 " pdb=" N LYS B 377 " model vdw 2.280 2.520 ... (remaining 76601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.240 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: 18.450 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.180 Find NCS groups from input model: 0.820 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- 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 10600 Z= 0.819 Angle : 0.879 15.804 14508 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 1.101 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: 0.2306 time to fit residues: 66.4129 Evaluate side-chains 199 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 134 optimal weight: 0.4980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10600 Z= 0.209 Angle : 0.506 5.144 14508 Z= 0.279 Chirality : 0.040 0.167 1727 Planarity : 0.005 0.057 1880 Dihedral : 8.515 125.539 1645 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.34 % Allowed : 16.57 % Favored : 80.09 % 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: 0.27 (0.22), residues: 1431 helix: 1.38 (0.19), residues: 689 sheet: -0.40 (0.41), residues: 161 loop : -1.10 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 487 HIS 0.003 0.001 HIS A 390 PHE 0.024 0.001 PHE A 327 TYR 0.011 0.001 TYR A 165 ARG 0.005 0.000 ARG A 368 *********************** 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 230 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7957 (t-100) cc_final: 0.7699 (t-100) REVERT: A 395 MET cc_start: 0.6578 (tpp) cc_final: 0.5908 (mpp) REVERT: B 94 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8064 (mtmt) REVERT: B 224 PHE cc_start: 0.8728 (t80) cc_final: 0.8493 (t80) REVERT: B 269 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: B 304 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.8027 (t) REVERT: B 318 GLU cc_start: 0.7944 (tt0) cc_final: 0.7675 (tt0) REVERT: B 340 SER cc_start: 0.8696 (p) cc_final: 0.8390 (t) REVERT: B 458 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 701 GLU cc_start: 0.7052 (tt0) cc_final: 0.6186 (tp30) outliers start: 30 outliers final: 18 residues processed: 214 average time/residue: 0.2322 time to fit residues: 69.4753 Evaluate side-chains 220 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP 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 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 294 SER 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 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 0.0970 chunk 45 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10600 Z= 0.224 Angle : 0.495 6.309 14508 Z= 0.270 Chirality : 0.040 0.193 1727 Planarity : 0.005 0.046 1880 Dihedral : 8.226 126.728 1643 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.67 % Allowed : 15.35 % Favored : 79.98 % 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: 0.18 (0.22), residues: 1431 helix: 1.25 (0.20), residues: 691 sheet: -0.46 (0.41), residues: 161 loop : -1.08 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.004 0.001 HIS A 390 PHE 0.020 0.001 PHE A 327 TYR 0.012 0.001 TYR B 453 ARG 0.007 0.001 ARG B 346 *********************** 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 246 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: A 215 ASP cc_start: 0.6060 (t0) cc_final: 0.5856 (t0) REVERT: A 367 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 395 MET cc_start: 0.6416 (tpp) cc_final: 0.5958 (tpp) REVERT: A 399 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 183 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7621 (ptp90) REVERT: B 226 LEU cc_start: 0.8694 (tp) cc_final: 0.8465 (tt) REVERT: B 269 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: B 301 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: B 340 SER cc_start: 0.8693 (p) cc_final: 0.8404 (t) REVERT: B 458 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7474 (t80) REVERT: B 473 TYR cc_start: 0.7891 (p90) cc_final: 0.7569 (p90) REVERT: B 701 GLU cc_start: 0.6962 (tt0) cc_final: 0.6109 (tp30) outliers start: 42 outliers final: 26 residues processed: 225 average time/residue: 0.2223 time to fit residues: 70.4711 Evaluate side-chains 230 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP 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 179 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 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 A residue 769 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 195 MET 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 294 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 307 SER 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 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 390 HIS A 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10600 Z= 0.286 Angle : 0.527 7.652 14508 Z= 0.288 Chirality : 0.042 0.188 1727 Planarity : 0.005 0.087 1880 Dihedral : 8.294 126.608 1643 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.89 % Allowed : 17.69 % Favored : 78.42 % 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: 0.02 (0.22), residues: 1431 helix: 1.11 (0.20), residues: 686 sheet: -0.50 (0.41), residues: 157 loop : -1.12 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 349 HIS 0.005 0.001 HIS A 390 PHE 0.024 0.002 PHE B 67 TYR 0.018 0.002 TYR A 734 ARG 0.006 0.000 ARG B 346 *********************** 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 237 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.212 Fit side-chains REVERT: A 367 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8015 (tt) REVERT: A 395 MET cc_start: 0.6494 (tpp) cc_final: 0.6096 (tpp) REVERT: A 399 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 701 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7692 (pm20) REVERT: B 55 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6819 (mt-10) REVERT: B 224 PHE cc_start: 0.8754 (t80) cc_final: 0.8493 (t80) REVERT: B 226 LEU cc_start: 0.8709 (tp) cc_final: 0.8472 (tt) REVERT: B 301 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7363 (mm-30) REVERT: B 318 GLU cc_start: 0.7922 (tt0) cc_final: 0.7662 (tt0) REVERT: B 340 SER cc_start: 0.8700 (p) cc_final: 0.8419 (t) REVERT: B 483 SER cc_start: 0.8959 (m) cc_final: 0.8699 (p) REVERT: B 614 PHE cc_start: 0.7530 (t80) cc_final: 0.7305 (t80) REVERT: B 701 GLU cc_start: 0.6966 (tt0) cc_final: 0.6037 (tp30) outliers start: 35 outliers final: 27 residues processed: 219 average time/residue: 0.2304 time to fit residues: 70.5024 Evaluate side-chains 227 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP 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 367 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 A residue 769 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 59 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10600 Z= 0.323 Angle : 0.546 9.012 14508 Z= 0.299 Chirality : 0.042 0.185 1727 Planarity : 0.005 0.078 1880 Dihedral : 8.416 126.547 1643 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.34 % Allowed : 19.13 % Favored : 76.53 % 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: -0.23 (0.22), residues: 1431 helix: 0.91 (0.20), residues: 682 sheet: -0.46 (0.40), residues: 165 loop : -1.31 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 349 HIS 0.005 0.001 HIS A 390 PHE 0.026 0.002 PHE B 67 TYR 0.021 0.002 TYR A 734 ARG 0.006 0.000 ARG B 346 *********************** 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 241 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.135 Fit side-chains REVERT: A 367 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 224 PHE cc_start: 0.8762 (t80) cc_final: 0.8504 (t80) REVERT: B 226 LEU cc_start: 0.8691 (tp) cc_final: 0.8483 (tt) REVERT: B 301 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 340 SER cc_start: 0.8695 (p) cc_final: 0.8418 (t) REVERT: B 458 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (t80) REVERT: B 473 TYR cc_start: 0.7926 (p90) cc_final: 0.7616 (p90) REVERT: B 483 SER cc_start: 0.9001 (m) cc_final: 0.8739 (p) REVERT: B 614 PHE cc_start: 0.7540 (t80) cc_final: 0.7314 (t80) REVERT: B 701 GLU cc_start: 0.7038 (tt0) cc_final: 0.6026 (tp30) outliers start: 39 outliers final: 27 residues processed: 225 average time/residue: 0.2192 time to fit residues: 69.0034 Evaluate side-chains 225 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP 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 367 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10600 Z= 0.196 Angle : 0.497 8.183 14508 Z= 0.269 Chirality : 0.040 0.195 1727 Planarity : 0.004 0.063 1880 Dihedral : 8.115 126.604 1643 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.00 % Allowed : 19.47 % Favored : 76.53 % 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: -0.02 (0.22), residues: 1431 helix: 1.16 (0.20), residues: 680 sheet: -0.47 (0.40), residues: 166 loop : -1.28 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 349 HIS 0.003 0.001 HIS A 396 PHE 0.017 0.001 PHE A 67 TYR 0.022 0.001 TYR A 734 ARG 0.005 0.000 ARG B 346 *********************** 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 237 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 367 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8010 (tt) REVERT: B 197 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 224 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80) REVERT: B 226 LEU cc_start: 0.8713 (tp) cc_final: 0.8492 (tt) REVERT: B 269 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 301 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 318 GLU cc_start: 0.7951 (tt0) cc_final: 0.7729 (tt0) REVERT: B 340 SER cc_start: 0.8688 (p) cc_final: 0.8428 (t) REVERT: B 458 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7453 (t80) REVERT: B 473 TYR cc_start: 0.7907 (p90) cc_final: 0.7609 (p90) REVERT: B 614 PHE cc_start: 0.7482 (t80) cc_final: 0.7280 (t80) REVERT: B 701 GLU cc_start: 0.6769 (tt0) cc_final: 0.5731 (tp30) outliers start: 36 outliers final: 22 residues processed: 220 average time/residue: 0.2279 time to fit residues: 69.7880 Evaluate side-chains 225 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP 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 367 LEU Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 195 MET 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 294 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 390 HIS A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10600 Z= 0.316 Angle : 0.548 7.838 14508 Z= 0.299 Chirality : 0.042 0.212 1727 Planarity : 0.005 0.065 1880 Dihedral : 8.323 126.755 1643 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.56 % Allowed : 20.36 % Favored : 76.08 % 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: -0.28 (0.22), residues: 1431 helix: 0.89 (0.20), residues: 687 sheet: -0.53 (0.40), residues: 163 loop : -1.37 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 349 HIS 0.004 0.001 HIS B 87 PHE 0.026 0.002 PHE B 67 TYR 0.019 0.002 TYR B 453 ARG 0.007 0.000 ARG B 346 *********************** 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 238 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7219 (mp0) cc_final: 0.6791 (mp0) REVERT: A 367 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 395 MET cc_start: 0.6885 (tpp) cc_final: 0.6374 (mpp) REVERT: A 414 ASN cc_start: 0.7975 (t0) cc_final: 0.7715 (t0) REVERT: B 197 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 224 PHE cc_start: 0.8770 (t80) cc_final: 0.8493 (t80) REVERT: B 226 LEU cc_start: 0.8704 (tp) cc_final: 0.8497 (tt) REVERT: B 239 GLU cc_start: 0.8215 (mp0) cc_final: 0.7871 (mp0) REVERT: B 301 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 318 GLU cc_start: 0.7918 (tt0) cc_final: 0.7673 (tt0) REVERT: B 340 SER cc_start: 0.8704 (p) cc_final: 0.8421 (t) REVERT: B 375 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6103 (tm-30) REVERT: B 458 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 473 TYR cc_start: 0.7919 (p90) cc_final: 0.7637 (p90) REVERT: B 609 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7409 (mt) REVERT: B 614 PHE cc_start: 0.7547 (t80) cc_final: 0.7301 (t80) REVERT: B 701 GLU cc_start: 0.6844 (tt0) cc_final: 0.5726 (tp30) outliers start: 32 outliers final: 26 residues processed: 222 average time/residue: 0.2492 time to fit residues: 78.8269 Evaluate side-chains 224 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP 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 367 LEU Chi-restraints excluded: chain A residue 390 HIS 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 95 ASP Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.0770 chunk 70 optimal weight: 0.0670 chunk 13 optimal weight: 0.0770 chunk 112 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 overall best weight: 0.1432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10600 Z= 0.155 Angle : 0.501 8.520 14508 Z= 0.268 Chirality : 0.039 0.212 1727 Planarity : 0.004 0.055 1880 Dihedral : 7.868 126.734 1643 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.56 % Allowed : 21.91 % Favored : 75.53 % 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: 0.12 (0.22), residues: 1431 helix: 1.33 (0.20), residues: 681 sheet: -0.45 (0.40), residues: 166 loop : -1.26 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 349 HIS 0.003 0.001 HIS B 390 PHE 0.015 0.001 PHE A 327 TYR 0.023 0.001 TYR A 734 ARG 0.006 0.000 ARG B 346 *********************** 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 fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: A 218 GLU cc_start: 0.7045 (mp0) cc_final: 0.6672 (mp0) REVERT: A 367 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 395 MET cc_start: 0.6896 (tpp) cc_final: 0.6531 (mpp) REVERT: A 414 ASN cc_start: 0.7769 (t0) cc_final: 0.7484 (t0) REVERT: B 106 VAL cc_start: 0.7790 (t) cc_final: 0.7588 (p) REVERT: B 197 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 226 LEU cc_start: 0.8681 (tp) cc_final: 0.8464 (tt) REVERT: B 301 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 318 GLU cc_start: 0.7945 (tt0) cc_final: 0.7691 (tt0) REVERT: B 340 SER cc_start: 0.8687 (p) cc_final: 0.8428 (t) REVERT: B 458 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7483 (t80) REVERT: B 609 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 614 PHE cc_start: 0.7423 (t80) cc_final: 0.7223 (t80) REVERT: B 701 GLU cc_start: 0.6755 (tt0) cc_final: 0.5716 (tp30) outliers start: 23 outliers final: 12 residues processed: 208 average time/residue: 0.2496 time to fit residues: 72.8250 Evaluate side-chains 209 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 HIS 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 B residue 95 ASP 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 390 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10600 Z= 0.259 Angle : 0.543 8.608 14508 Z= 0.291 Chirality : 0.041 0.206 1727 Planarity : 0.005 0.060 1880 Dihedral : 8.017 126.810 1643 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.00 % Allowed : 22.25 % Favored : 75.75 % 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: -0.02 (0.22), residues: 1431 helix: 1.21 (0.20), residues: 675 sheet: -0.46 (0.40), residues: 166 loop : -1.32 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 349 HIS 0.003 0.001 HIS B 87 PHE 0.021 0.002 PHE A 67 TYR 0.017 0.001 TYR A 419 ARG 0.006 0.000 ARG B 346 *********************** 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 216 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7132 (mp0) cc_final: 0.6698 (mp0) REVERT: A 367 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 395 MET cc_start: 0.6996 (tpp) cc_final: 0.6480 (mpp) REVERT: B 226 LEU cc_start: 0.8701 (tp) cc_final: 0.8490 (tt) REVERT: B 301 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 340 SER cc_start: 0.8695 (p) cc_final: 0.8427 (t) REVERT: B 458 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 473 TYR cc_start: 0.7936 (p90) cc_final: 0.7642 (p90) REVERT: B 609 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7325 (mt) REVERT: B 614 PHE cc_start: 0.7457 (t80) cc_final: 0.7246 (t80) REVERT: B 701 GLU cc_start: 0.6810 (tt0) cc_final: 0.5712 (tp30) outliers start: 18 outliers final: 13 residues processed: 207 average time/residue: 0.2331 time to fit residues: 66.9319 Evaluate side-chains 207 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 HIS 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 B residue 95 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 117 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10600 Z= 0.211 Angle : 0.526 8.327 14508 Z= 0.281 Chirality : 0.040 0.218 1727 Planarity : 0.004 0.054 1880 Dihedral : 7.951 126.945 1643 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.89 % Allowed : 22.69 % Favored : 75.42 % 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: 0.03 (0.22), residues: 1431 helix: 1.24 (0.20), residues: 674 sheet: -0.38 (0.40), residues: 170 loop : -1.30 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 349 HIS 0.002 0.001 HIS A 87 PHE 0.018 0.001 PHE A 67 TYR 0.020 0.001 TYR A 734 ARG 0.007 0.000 ARG B 346 ********************** 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 214 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7099 (mp0) cc_final: 0.6677 (mp0) REVERT: A 367 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 395 MET cc_start: 0.6898 (tpp) cc_final: 0.6450 (mpp) REVERT: A 414 ASN cc_start: 0.7923 (t0) cc_final: 0.7622 (t0) REVERT: A 619 MET cc_start: 0.6803 (tpt) cc_final: 0.6568 (tpt) REVERT: B 156 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7885 (ttp-170) REVERT: B 197 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7343 (mm-30) REVERT: B 226 LEU cc_start: 0.8696 (tp) cc_final: 0.8479 (tt) REVERT: B 301 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 318 GLU cc_start: 0.7932 (tt0) cc_final: 0.7691 (tt0) REVERT: B 340 SER cc_start: 0.8694 (p) cc_final: 0.8440 (t) REVERT: B 458 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7423 (t80) REVERT: B 473 TYR cc_start: 0.7946 (p90) cc_final: 0.7625 (p90) REVERT: B 609 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7280 (mt) REVERT: B 614 PHE cc_start: 0.7443 (t80) cc_final: 0.7233 (t80) REVERT: B 701 GLU cc_start: 0.6715 (tt0) cc_final: 0.5635 (tp30) outliers start: 17 outliers final: 12 residues processed: 206 average time/residue: 0.2377 time to fit residues: 67.5756 Evaluate side-chains 212 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.0040 chunk 117 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121170 restraints weight = 19438.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124641 restraints weight = 10606.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126907 restraints weight = 7093.852| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 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 = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10600 Z= 0.213 Angle : 0.531 8.204 14508 Z= 0.284 Chirality : 0.040 0.216 1727 Planarity : 0.005 0.096 1880 Dihedral : 7.907 126.704 1643 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.89 % Allowed : 22.69 % Favored : 75.42 % 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: 0.08 (0.22), residues: 1431 helix: 1.25 (0.20), residues: 677 sheet: -0.41 (0.40), residues: 164 loop : -1.22 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 349 HIS 0.002 0.001 HIS A 87 PHE 0.018 0.001 PHE A 67 TYR 0.018 0.001 TYR A 419 ARG 0.007 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.77 seconds wall clock time: 46 minutes 53.00 seconds (2813.00 seconds total)