Starting phenix.real_space_refine (version: dev) on Sun Feb 19 16:30:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/02_2023/7mtq_23994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/02_2023/7mtq_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_23994/02_2023/7mtq_23994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/02_2023/7mtq_23994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/02_2023/7mtq_23994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtq_23994/02_2023/7mtq_23994_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-dev-4877/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 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 chiralities: 1 Time building chain proxies: 6.59, per 1000 atoms: 0.63 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: 4.74 Conformation dependent library (CDL) restraints added in 1.8 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: 1.68 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: 3.12 Time building geometry restraints manager: 5.07 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 - 17.38: 5634 17.38 - 34.76: 428 34.76 - 52.14: 117 52.14 - 69.53: 13 69.53 - 86.91: 3 Dihedral angle restraints: 6195 sinusoidal: 1906 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 6192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1545 0.078 - 0.157: 152 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 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. 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: 4.600 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: 0.000 Extract box with map and model: 18.240 Check model and map are aligned: 0.180 Process input model: 31.560 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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= 0.818 Angle : 0.876 15.804 14508 Z= 0.543 Chirality : 0.054 0.392 1727 Planarity : 0.008 0.227 1880 Dihedral : 13.695 79.249 3379 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 % 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 *********************** 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 : 1.168 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 207 average time/residue: 0.2363 time to fit residues: 68.2466 Evaluate side-chains 202 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0997 time to fit residues: 2.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 0.7323 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10600 Z= 0.207 Angle : 0.507 5.093 14508 Z= 0.281 Chirality : 0.040 0.167 1727 Planarity : 0.005 0.057 1880 Dihedral : 5.370 60.338 1571 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.67 % 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: 1.33 (0.20), residues: 689 sheet: -0.42 (0.41), residues: 161 loop : -1.10 (0.24), residues: 581 *********************** 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 233 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.131 Fit side-chains outliers start: 33 outliers final: 20 residues processed: 215 average time/residue: 0.2431 time to fit residues: 74.3066 Evaluate side-chains 221 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1079 time to fit residues: 5.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 91 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 134 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10600 Z= 0.150 Angle : 0.471 5.477 14508 Z= 0.256 Chirality : 0.039 0.191 1727 Planarity : 0.004 0.045 1880 Dihedral : 5.051 59.322 1571 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1431 helix: 1.34 (0.20), residues: 695 sheet: -0.30 (0.41), residues: 161 loop : -0.99 (0.25), residues: 575 *********************** 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 215 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 1.311 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 209 average time/residue: 0.2360 time to fit residues: 69.8612 Evaluate side-chains 197 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1283 time to fit residues: 2.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10600 Z= 0.284 Angle : 0.535 7.206 14508 Z= 0.293 Chirality : 0.041 0.194 1727 Planarity : 0.005 0.088 1880 Dihedral : 5.312 62.769 1571 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.22), residues: 1431 helix: 1.15 (0.20), residues: 692 sheet: -0.47 (0.41), residues: 159 loop : -0.99 (0.24), residues: 580 *********************** 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 229 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.251 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 214 average time/residue: 0.2439 time to fit residues: 73.3656 Evaluate side-chains 208 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1077 time to fit residues: 4.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 77 HIS A 332 GLN A 390 HIS A 414 ASN B 593 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 10600 Z= 0.488 Angle : 0.653 8.481 14508 Z= 0.363 Chirality : 0.046 0.217 1727 Planarity : 0.006 0.082 1880 Dihedral : 5.983 66.299 1571 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.21), residues: 1431 helix: 0.35 (0.19), residues: 693 sheet: -0.56 (0.42), residues: 148 loop : -1.32 (0.24), residues: 590 *********************** 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 223 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.363 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 213 average time/residue: 0.2395 time to fit residues: 71.5306 Evaluate side-chains 207 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1006 time to fit residues: 3.1881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 83 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2100 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= 0.237 Angle : 0.533 5.857 14508 Z= 0.291 Chirality : 0.041 0.201 1727 Planarity : 0.005 0.065 1880 Dihedral : 5.503 63.119 1571 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.78 % 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: -0.34 (0.22), residues: 1431 helix: 0.84 (0.20), residues: 681 sheet: -0.62 (0.40), residues: 159 loop : -1.35 (0.24), residues: 591 *********************** 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 220 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.232 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 207 average time/residue: 0.2693 time to fit residues: 77.5461 Evaluate side-chains 208 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1350 time to fit residues: 4.1938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.0000 chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 0.1980 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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: 0.7352 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10600 Z= 0.217 Angle : 0.528 7.670 14508 Z= 0.286 Chirality : 0.040 0.217 1727 Planarity : 0.005 0.063 1880 Dihedral : 5.306 62.626 1571 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.22 % 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: 0.99 (0.20), residues: 679 sheet: -0.64 (0.41), residues: 154 loop : -1.33 (0.24), residues: 598 *********************** 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 208 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.221 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 203 average time/residue: 0.2464 time to fit residues: 69.9932 Evaluate side-chains 200 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0988 time to fit residues: 2.9929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.0040 chunk 70 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 overall best weight: 0.3470 ------------------------------------------------------------------------------- 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: 0.7329 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10600 Z= 0.192 Angle : 0.528 6.715 14508 Z= 0.286 Chirality : 0.041 0.231 1727 Planarity : 0.004 0.058 1880 Dihedral : 5.188 61.679 1571 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.22), residues: 1431 helix: 1.16 (0.20), residues: 680 sheet: -0.56 (0.41), residues: 154 loop : -1.31 (0.24), residues: 597 *********************** 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 203 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.266 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 199 average time/residue: 0.2593 time to fit residues: 72.3120 Evaluate side-chains 190 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1165 time to fit residues: 2.2068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 10600 Z= 0.360 Angle : 0.615 9.905 14508 Z= 0.333 Chirality : 0.043 0.206 1727 Planarity : 0.005 0.062 1880 Dihedral : 5.570 64.436 1571 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.22), residues: 1431 helix: 0.72 (0.20), residues: 689 sheet: -0.45 (0.41), residues: 155 loop : -1.43 (0.24), residues: 587 *********************** 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 199 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.238 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 194 average time/residue: 0.2499 time to fit residues: 67.7429 Evaluate side-chains 184 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1068 time to fit residues: 2.6093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 12 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.0870 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10600 Z= 0.177 Angle : 0.547 9.031 14508 Z= 0.292 Chirality : 0.040 0.236 1727 Planarity : 0.004 0.055 1880 Dihedral : 5.188 61.603 1571 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.22 % 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: -0.10 (0.22), residues: 1431 helix: 1.10 (0.20), residues: 682 sheet: -0.44 (0.41), residues: 165 loop : -1.34 (0.24), residues: 584 ********************** 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 190 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.103 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.2635 time to fit residues: 68.8107 Evaluate side-chains 188 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1382 time to fit residues: 1.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0030 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119649 restraints weight = 19418.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122976 restraints weight = 10768.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125240 restraints weight = 7242.535| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2653 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= 0.219 Angle : 0.571 9.034 14508 Z= 0.303 Chirality : 0.041 0.216 1727 Planarity : 0.005 0.058 1880 Dihedral : 5.175 62.101 1571 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.44 % 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: 1.05 (0.20), residues: 684 sheet: -0.48 (0.43), residues: 146 loop : -1.29 (0.24), residues: 601 =============================================================================== Job complete usr+sys time: 2443.62 seconds wall clock time: 45 minutes 15.29 seconds (2715.29 seconds total)