Starting phenix.real_space_refine on Thu Feb 15 11:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjy_33237/02_2024/7xjy_33237.pdb" } resolution = 3.6 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= 0.133 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 48 5.16 5 C 7713 2.51 5 N 2061 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 815": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12070 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6034 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6036 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 6.49, per 1000 atoms: 0.54 Number of scatterers: 12070 At special positions: 0 Unit cell: (150.7, 122.1, 86.9, 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 48 16.00 O 2248 8.00 N 2061 7.00 C 7713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 16 sheets defined 54.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.834A pdb=" N ALA A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 47 " --> pdb=" O TRP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.545A pdb=" N SER A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.502A pdb=" N GLY A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.512A pdb=" N ASN A 205 " --> pdb=" O HIS A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.540A pdb=" N GLU A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASN A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.638A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.912A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 311 removed outlier: 4.071A pdb=" N ARG A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 Processing helix chain 'A' and resid 466 through 480 Proline residue: A 474 - end of helix removed outlier: 3.601A pdb=" N ILE A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 549 Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 580 through 591 removed outlier: 3.723A pdb=" N VAL A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.778A pdb=" N PHE A 605 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.685A pdb=" N LEU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 673 removed outlier: 3.591A pdb=" N VAL A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.003A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.828A pdb=" N SER A 686 " --> pdb=" O ASP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 745 through 748 removed outlier: 3.588A pdb=" N ALA A 748 " --> pdb=" O THR A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 748' Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 762 through 772 Processing helix chain 'A' and resid 785 through 807 Processing helix chain 'A' and resid 818 through 833 removed outlier: 3.558A pdb=" N ILE A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.503A pdb=" N GLU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.856A pdb=" N ALA B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.551A pdb=" N SER B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.507A pdb=" N ASN B 205 " --> pdb=" O HIS B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 214 through 231 removed outlier: 5.743A pdb=" N GLU B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.696A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.899A pdb=" N ALA B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 removed outlier: 4.093A pdb=" N ARG B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 376 Processing helix chain 'B' and resid 466 through 480 Proline residue: B 474 - end of helix removed outlier: 3.641A pdb=" N ILE B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 541 through 549 removed outlier: 3.504A pdb=" N ALA B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 580 through 591 removed outlier: 3.747A pdb=" N VAL B 591 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.787A pdb=" N PHE B 605 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.697A pdb=" N LEU B 613 " --> pdb=" O PRO B 609 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 674 removed outlier: 3.595A pdb=" N VAL B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 687 removed outlier: 3.829A pdb=" N SER B 686 " --> pdb=" O ASP B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'B' and resid 707 through 715 Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 745 through 748 removed outlier: 3.526A pdb=" N ALA B 748 " --> pdb=" O THR B 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 748' Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 762 through 772 Processing helix chain 'B' and resid 785 through 807 Processing helix chain 'B' and resid 819 through 833 Processing helix chain 'B' and resid 838 through 850 Processing helix chain 'B' and resid 855 through 874 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.386A pdb=" N ALA A 49 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL A 82 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 165 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET A 160 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 166 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 152 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.386A pdb=" N ALA A 49 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL A 82 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 165 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET A 160 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 166 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 152 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 153 " --> pdb=" O TRP A 144 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 144 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 388 removed outlier: 4.223A pdb=" N ASN A 398 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG A 342 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.605A pdb=" N PHE A 514 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 577 removed outlier: 6.923A pdb=" N PHE A 624 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS A 637 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL A 626 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 3.578A pdb=" N HIS A 691 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.345A pdb=" N ALA B 49 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL B 82 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 165 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 160 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 166 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 152 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.345A pdb=" N ALA B 49 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL B 82 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 165 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 160 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 166 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 152 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 153 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 144 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AB3, first strand: chain 'B' and resid 383 through 388 removed outlier: 4.202A pdb=" N ASN B 398 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG B 342 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 514 removed outlier: 3.599A pdb=" N PHE B 514 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 522 through 524 Processing sheet with id=AB6, first strand: chain 'B' and resid 575 through 577 removed outlier: 6.994A pdb=" N PHE B 624 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N CYS B 637 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 626 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 689 through 691 removed outlier: 3.710A pdb=" N HIS B 691 " --> pdb=" O GLY B 695 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2058 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: 4.06 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2035 1.27 - 1.41: 2971 1.41 - 1.54: 7217 1.54 - 1.68: 15 1.68 - 1.81: 82 Bond restraints: 12320 Sorted by residual: bond pdb=" C TYR B 208 " pdb=" O TYR B 208 " ideal model delta sigma weight residual 1.236 1.140 0.097 1.15e-02 7.56e+03 7.05e+01 bond pdb=" C GLN A 33 " pdb=" N GLN A 34 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" C GLN A 33 " pdb=" O GLN A 33 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 1.522 1.470 0.051 1.24e-02 6.50e+03 1.72e+01 bond pdb=" C THR B 209 " pdb=" N LYS B 210 " ideal model delta sigma weight residual 1.332 1.278 0.055 1.40e-02 5.10e+03 1.52e+01 ... (remaining 12315 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 275 105.60 - 112.70: 6452 112.70 - 119.80: 4406 119.80 - 126.91: 5433 126.91 - 134.01: 138 Bond angle restraints: 16704 Sorted by residual: angle pdb=" N GLY A 807 " pdb=" CA GLY A 807 " pdb=" C GLY A 807 " ideal model delta sigma weight residual 111.85 120.10 -8.25 1.20e+00 6.94e-01 4.73e+01 angle pdb=" N GLY B 807 " pdb=" CA GLY B 807 " pdb=" C GLY B 807 " ideal model delta sigma weight residual 111.63 118.57 -6.94 1.15e+00 7.56e-01 3.64e+01 angle pdb=" CA GLY B 807 " pdb=" C GLY B 807 " pdb=" O GLY B 807 " ideal model delta sigma weight residual 122.16 117.36 4.80 8.20e-01 1.49e+00 3.43e+01 angle pdb=" CA GLY A 807 " pdb=" C GLY A 807 " pdb=" O GLY A 807 " ideal model delta sigma weight residual 122.13 117.20 4.93 8.90e-01 1.26e+00 3.07e+01 angle pdb=" N ASP A 673 " pdb=" CA ASP A 673 " pdb=" C ASP A 673 " ideal model delta sigma weight residual 112.93 106.76 6.17 1.12e+00 7.97e-01 3.04e+01 ... (remaining 16699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6694 17.55 - 35.10: 537 35.10 - 52.65: 139 52.65 - 70.20: 44 70.20 - 87.76: 8 Dihedral angle restraints: 7422 sinusoidal: 3004 harmonic: 4418 Sorted by residual: dihedral pdb=" CA LYS B 647 " pdb=" C LYS B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LYS A 647 " pdb=" C LYS A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" C MET A 672 " pdb=" N MET A 672 " pdb=" CA MET A 672 " pdb=" CB MET A 672 " ideal model delta harmonic sigma weight residual -122.60 -111.28 -11.32 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1510 0.062 - 0.125: 315 0.125 - 0.187: 46 0.187 - 0.250: 16 0.250 - 0.312: 7 Chirality restraints: 1894 Sorted by residual: chirality pdb=" CB THR B 209 " pdb=" CA THR B 209 " pdb=" OG1 THR B 209 " pdb=" CG2 THR B 209 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB THR A 209 " pdb=" CA THR A 209 " pdb=" OG1 THR A 209 " pdb=" CG2 THR A 209 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA THR B 209 " pdb=" N THR B 209 " pdb=" C THR B 209 " pdb=" CB THR B 209 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1891 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 208 " -0.058 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR A 208 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 208 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 208 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 208 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 208 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 208 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 208 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 208 " 0.054 2.00e-02 2.50e+03 2.88e-02 1.66e+01 pdb=" CG TYR B 208 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 208 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 208 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 208 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 208 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 208 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 208 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 33 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLN A 33 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 33 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN A 34 " 0.025 2.00e-02 2.50e+03 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1232 2.74 - 3.28: 11948 3.28 - 3.82: 19021 3.82 - 4.36: 22739 4.36 - 4.90: 39436 Nonbonded interactions: 94376 Sorted by model distance: nonbonded pdb=" OE1 GLU A 347 " pdb=" OH TYR A 542 " model vdw 2.197 2.440 nonbonded pdb=" O LEU A 30 " pdb=" NE2 GLN A 198 " model vdw 2.198 2.520 nonbonded pdb=" O ASN B 833 " pdb=" NZ LYS B 835 " model vdw 2.207 2.520 nonbonded pdb=" OG1 THR A 350 " pdb=" O GLU A 351 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU B 347 " pdb=" OH TYR B 542 " model vdw 2.217 2.440 ... (remaining 94371 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 28 through 679 or (resid 680 and (name N or name CA or nam \ e C or name O or name CB )) or resid 681 through 874)) selection = (chain 'B' and (resid 28 through 820 or (resid 821 and (name N or name CA or nam \ e C or name O or name CB )) or resid 822 through 874)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.520 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: 15.960 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.470 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 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 : 0.007 0.097 12320 Z= 0.471 Angle : 0.936 9.965 16704 Z= 0.617 Chirality : 0.057 0.312 1894 Planarity : 0.006 0.053 2158 Dihedral : 14.445 87.755 4566 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.16 % Favored : 95.51 % Rotamer: Outliers : 7.59 % Allowed : 10.93 % Favored : 81.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 8.82 % 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 (0.21), residues: 1514 helix: 0.99 (0.19), residues: 750 sheet: -0.53 (0.37), residues: 184 loop : -1.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 43 HIS 0.007 0.001 HIS A 356 PHE 0.017 0.002 PHE A 668 TYR 0.058 0.004 TYR A 208 ARG 0.004 0.000 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 232 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 125 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 253 LEU cc_start: 0.6498 (mt) cc_final: 0.6295 (mt) REVERT: A 263 ASP cc_start: 0.8084 (t70) cc_final: 0.7757 (t0) REVERT: B 30 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7448 (mp) REVERT: B 118 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 183 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 253 LEU cc_start: 0.6500 (mt) cc_final: 0.6260 (mt) REVERT: B 263 ASP cc_start: 0.7974 (t70) cc_final: 0.7655 (t0) REVERT: B 366 GLU cc_start: 0.7707 (tt0) cc_final: 0.7468 (tt0) REVERT: B 500 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.5403 (p-90) outliers start: 100 outliers final: 48 residues processed: 324 average time/residue: 0.2656 time to fit residues: 118.9956 Evaluate side-chains 189 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 813 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 809 GLN B 33 GLN B 98 ASN B 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12320 Z= 0.177 Angle : 0.561 6.803 16704 Z= 0.300 Chirality : 0.043 0.152 1894 Planarity : 0.005 0.045 2158 Dihedral : 8.297 61.680 1727 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 4.02 % Allowed : 16.24 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 0.60 (0.22), residues: 1514 helix: 1.38 (0.19), residues: 774 sheet: -0.10 (0.39), residues: 182 loop : -0.77 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 43 HIS 0.003 0.001 HIS A 544 PHE 0.013 0.001 PHE A 534 TYR 0.017 0.002 TYR A 188 ARG 0.004 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 371 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 744 PHE cc_start: 0.7345 (m-80) cc_final: 0.6974 (m-80) REVERT: B 30 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7131 (mp) REVERT: B 253 LEU cc_start: 0.6286 (mt) cc_final: 0.6043 (mt) REVERT: B 366 GLU cc_start: 0.7676 (tt0) cc_final: 0.7425 (tt0) REVERT: B 500 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.6395 (p90) REVERT: B 634 LEU cc_start: 0.8491 (mm) cc_final: 0.8149 (mt) REVERT: B 672 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7201 (tmm) outliers start: 53 outliers final: 28 residues processed: 196 average time/residue: 0.2382 time to fit residues: 67.1455 Evaluate side-chains 166 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 12320 Z= 0.159 Angle : 0.509 7.117 16704 Z= 0.269 Chirality : 0.042 0.144 1894 Planarity : 0.004 0.045 2158 Dihedral : 6.408 58.666 1682 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 3.34 % Allowed : 17.07 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.12 (0.22), residues: 1514 helix: 1.90 (0.19), residues: 760 sheet: 0.27 (0.41), residues: 170 loop : -0.64 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.005 0.001 HIS B 544 PHE 0.012 0.001 PHE A 245 TYR 0.014 0.001 TYR B 188 ARG 0.007 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 697 MET cc_start: 0.5302 (mtp) cc_final: 0.5085 (mtp) REVERT: A 744 PHE cc_start: 0.7413 (m-80) cc_final: 0.6771 (m-80) REVERT: B 183 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8830 (p) REVERT: B 253 LEU cc_start: 0.6140 (mt) cc_final: 0.5906 (mt) REVERT: B 366 GLU cc_start: 0.7701 (tt0) cc_final: 0.7435 (tt0) REVERT: B 500 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.5188 (p-90) REVERT: B 634 LEU cc_start: 0.8553 (mm) cc_final: 0.8332 (mt) REVERT: B 639 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7518 (mp) REVERT: B 672 MET cc_start: 0.7382 (tmm) cc_final: 0.7019 (tmm) outliers start: 44 outliers final: 25 residues processed: 199 average time/residue: 0.2402 time to fit residues: 68.9747 Evaluate side-chains 170 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12320 Z= 0.291 Angle : 0.597 8.687 16704 Z= 0.317 Chirality : 0.045 0.162 1894 Planarity : 0.005 0.048 2158 Dihedral : 6.093 59.994 1670 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 4.55 % Allowed : 18.13 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 0.70 (0.22), residues: 1514 helix: 1.58 (0.19), residues: 770 sheet: -0.09 (0.38), residues: 188 loop : -0.89 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 43 HIS 0.005 0.001 HIS B 356 PHE 0.018 0.002 PHE B 534 TYR 0.024 0.002 TYR A 188 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 140 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 391 ARG cc_start: 0.6485 (ptp90) cc_final: 0.6238 (ptp-110) REVERT: A 634 LEU cc_start: 0.8632 (mm) cc_final: 0.8356 (mt) REVERT: A 639 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 668 PHE cc_start: 0.7486 (t80) cc_final: 0.7000 (t80) REVERT: A 680 GLU cc_start: 0.7509 (mp0) cc_final: 0.6965 (pm20) REVERT: A 744 PHE cc_start: 0.7491 (m-80) cc_final: 0.7141 (m-80) REVERT: B 183 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 253 LEU cc_start: 0.6471 (mt) cc_final: 0.6215 (mt) REVERT: B 500 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.5354 (p-90) REVERT: B 634 LEU cc_start: 0.8603 (mm) cc_final: 0.8400 (mt) REVERT: B 672 MET cc_start: 0.7549 (tmm) cc_final: 0.7076 (tmm) outliers start: 60 outliers final: 35 residues processed: 195 average time/residue: 0.2386 time to fit residues: 67.6223 Evaluate side-chains 165 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12320 Z= 0.160 Angle : 0.517 7.920 16704 Z= 0.270 Chirality : 0.042 0.144 1894 Planarity : 0.004 0.045 2158 Dihedral : 5.513 59.312 1664 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 3.49 % Allowed : 18.44 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.04 (0.22), residues: 1514 helix: 1.89 (0.19), residues: 760 sheet: 0.04 (0.40), residues: 182 loop : -0.72 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS A 103 PHE 0.012 0.001 PHE B 668 TYR 0.016 0.001 TYR A 188 ARG 0.006 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 LEU cc_start: 0.8527 (mm) cc_final: 0.8302 (mt) REVERT: A 639 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7734 (mp) REVERT: A 668 PHE cc_start: 0.7370 (t80) cc_final: 0.6914 (t80) REVERT: A 680 GLU cc_start: 0.7250 (mp0) cc_final: 0.6863 (pm20) REVERT: A 744 PHE cc_start: 0.7510 (m-80) cc_final: 0.6771 (m-80) REVERT: B 253 LEU cc_start: 0.6270 (mt) cc_final: 0.6055 (mt) REVERT: B 500 TRP cc_start: 0.6564 (OUTLIER) cc_final: 0.5211 (p-90) REVERT: B 639 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7563 (mp) REVERT: B 672 MET cc_start: 0.7391 (tmm) cc_final: 0.6947 (tmm) REVERT: B 685 LEU cc_start: 0.6336 (tp) cc_final: 0.6063 (tp) outliers start: 46 outliers final: 33 residues processed: 183 average time/residue: 0.2377 time to fit residues: 63.0607 Evaluate side-chains 163 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN A 833 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12320 Z= 0.249 Angle : 0.571 9.348 16704 Z= 0.298 Chirality : 0.043 0.158 1894 Planarity : 0.005 0.047 2158 Dihedral : 5.263 59.001 1660 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 4.40 % Allowed : 18.97 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 0.88 (0.22), residues: 1514 helix: 1.74 (0.19), residues: 760 sheet: -0.11 (0.38), residues: 196 loop : -0.75 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.004 0.001 HIS B 356 PHE 0.014 0.001 PHE B 534 TYR 0.020 0.002 TYR A 188 ARG 0.019 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 130 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 391 ARG cc_start: 0.6330 (ptp90) cc_final: 0.6128 (ptp-110) REVERT: A 639 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 668 PHE cc_start: 0.7473 (t80) cc_final: 0.7037 (t80) REVERT: B 183 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8838 (p) REVERT: B 253 LEU cc_start: 0.6426 (mt) cc_final: 0.6211 (mt) REVERT: B 500 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.5394 (p-90) REVERT: B 639 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7701 (mp) REVERT: B 672 MET cc_start: 0.7485 (tmm) cc_final: 0.7017 (tmm) REVERT: B 685 LEU cc_start: 0.6646 (tp) cc_final: 0.6276 (tp) outliers start: 58 outliers final: 43 residues processed: 183 average time/residue: 0.2417 time to fit residues: 64.5232 Evaluate side-chains 165 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 118 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.6975 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12320 Z= 0.151 Angle : 0.529 10.289 16704 Z= 0.270 Chirality : 0.042 0.160 1894 Planarity : 0.004 0.048 2158 Dihedral : 5.079 59.512 1660 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 3.11 % Allowed : 20.49 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.12 (0.22), residues: 1514 helix: 1.93 (0.19), residues: 762 sheet: 0.15 (0.40), residues: 182 loop : -0.67 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS B 103 PHE 0.022 0.001 PHE A 770 TYR 0.014 0.001 TYR A 188 ARG 0.009 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 MET cc_start: 0.8546 (ptm) cc_final: 0.8302 (ptt) REVERT: A 639 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 668 PHE cc_start: 0.7403 (t80) cc_final: 0.6945 (t80) REVERT: B 183 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8822 (p) REVERT: B 253 LEU cc_start: 0.6259 (mt) cc_final: 0.6048 (mt) REVERT: B 500 TRP cc_start: 0.6570 (OUTLIER) cc_final: 0.5177 (p-90) REVERT: B 639 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7652 (mp) REVERT: B 672 MET cc_start: 0.7371 (tmm) cc_final: 0.6912 (tmm) REVERT: B 685 LEU cc_start: 0.6764 (tp) cc_final: 0.6396 (tp) outliers start: 41 outliers final: 28 residues processed: 166 average time/residue: 0.2399 time to fit residues: 57.8728 Evaluate side-chains 156 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12320 Z= 0.190 Angle : 0.543 10.850 16704 Z= 0.280 Chirality : 0.043 0.151 1894 Planarity : 0.004 0.049 2158 Dihedral : 4.903 58.933 1656 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 21.02 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.06 (0.22), residues: 1514 helix: 1.87 (0.19), residues: 772 sheet: 0.15 (0.40), residues: 182 loop : -0.75 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.003 0.001 HIS A 356 PHE 0.012 0.001 PHE B 668 TYR 0.017 0.002 TYR A 188 ARG 0.005 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 668 PHE cc_start: 0.7412 (t80) cc_final: 0.6985 (t80) REVERT: A 744 PHE cc_start: 0.6941 (m-80) cc_final: 0.6705 (m-80) REVERT: B 183 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8838 (p) REVERT: B 253 LEU cc_start: 0.6310 (mt) cc_final: 0.6098 (mt) REVERT: B 639 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7653 (mp) REVERT: B 672 MET cc_start: 0.7416 (tmm) cc_final: 0.6910 (tmm) REVERT: B 685 LEU cc_start: 0.6687 (tp) cc_final: 0.6126 (tp) outliers start: 41 outliers final: 34 residues processed: 161 average time/residue: 0.2385 time to fit residues: 55.7847 Evaluate side-chains 157 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12320 Z= 0.155 Angle : 0.533 10.767 16704 Z= 0.273 Chirality : 0.042 0.190 1894 Planarity : 0.004 0.046 2158 Dihedral : 4.713 59.191 1654 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 2.88 % Allowed : 21.24 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.24 (0.22), residues: 1514 helix: 1.98 (0.19), residues: 768 sheet: 0.27 (0.40), residues: 182 loop : -0.59 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS A 103 PHE 0.016 0.001 PHE B 668 TYR 0.014 0.001 TYR A 188 ARG 0.005 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 668 PHE cc_start: 0.7384 (t80) cc_final: 0.6955 (t80) REVERT: A 744 PHE cc_start: 0.6914 (m-80) cc_final: 0.6631 (m-80) REVERT: B 183 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 253 LEU cc_start: 0.6241 (mt) cc_final: 0.6027 (mt) REVERT: B 500 TRP cc_start: 0.6560 (OUTLIER) cc_final: 0.5126 (p-90) REVERT: B 639 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7626 (mp) REVERT: B 672 MET cc_start: 0.7342 (tmm) cc_final: 0.6868 (tmm) outliers start: 38 outliers final: 28 residues processed: 166 average time/residue: 0.2386 time to fit residues: 57.8970 Evaluate side-chains 156 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 93 optimal weight: 0.0980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 618 GLN A 833 ASN B 172 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12320 Z= 0.145 Angle : 0.522 10.597 16704 Z= 0.269 Chirality : 0.042 0.172 1894 Planarity : 0.004 0.045 2158 Dihedral : 4.605 57.238 1652 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 2.35 % Allowed : 22.00 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 1.24 (0.22), residues: 1514 helix: 2.00 (0.19), residues: 780 sheet: 0.34 (0.40), residues: 182 loop : -0.71 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.002 0.000 HIS A 103 PHE 0.018 0.001 PHE B 668 TYR 0.013 0.001 TYR A 188 ARG 0.008 0.000 ARG A 796 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 MET cc_start: 0.8539 (ptm) cc_final: 0.8210 (ptt) REVERT: A 668 PHE cc_start: 0.7396 (t80) cc_final: 0.6995 (t80) REVERT: A 744 PHE cc_start: 0.6882 (m-80) cc_final: 0.6612 (m-80) REVERT: B 253 LEU cc_start: 0.6214 (mt) cc_final: 0.6006 (mt) REVERT: B 576 ASP cc_start: 0.6426 (m-30) cc_final: 0.6164 (m-30) REVERT: B 672 MET cc_start: 0.7318 (tmm) cc_final: 0.6824 (tmm) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.2448 time to fit residues: 57.0342 Evaluate side-chains 154 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 ASN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145019 restraints weight = 19983.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144823 restraints weight = 14772.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145691 restraints weight = 13736.668| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 12320 Z= 0.234 Angle : 0.824 59.200 16704 Z= 0.486 Chirality : 0.042 0.221 1894 Planarity : 0.004 0.049 2158 Dihedral : 4.640 57.191 1652 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 22.00 % Favored : 75.57 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.82 % 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: 1.24 (0.22), residues: 1514 helix: 2.00 (0.19), residues: 778 sheet: 0.34 (0.40), residues: 182 loop : -0.70 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.002 0.000 HIS A 103 PHE 0.012 0.001 PHE B 668 TYR 0.013 0.001 TYR A 188 ARG 0.011 0.000 ARG A 796 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.36 seconds wall clock time: 45 minutes 10.96 seconds (2710.96 seconds total)