Starting phenix.real_space_refine on Sun Mar 17 21:44:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gam_8011/03_2024/5gam_8011_updated.pdb" } resolution = 3.7 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 169 5.49 5 S 56 5.16 5 C 11662 2.51 5 N 3310 2.21 5 O 3926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "b ARG 11": "NH1" <-> "NH2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "g ARG 30": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j GLU 70": "OE1" <-> "OE2" Residue "j ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19123 Number of models: 1 Model: "" Number of chains: 13 Chain: "U" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 64, 'rna3p_pyr': 58} Link IDs: {'rna2p': 18, 'rna3p': 122} Chain breaks: 2 Chain: "A" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4702 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 39, 'TRANS': 550} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 6450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6450 Classifications: {'peptide': 855} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'CIS': 8, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 800} Chain breaks: 3 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 34, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 265 Chain: "W" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 532 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain breaks: 1 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "x" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.75, per 1000 atoms: 0.56 Number of scatterers: 19123 At special positions: 0 Unit cell: (138.71, 143, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 169 15.00 O 3926 8.00 N 3310 7.00 C 11662 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: 8.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3842 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 25 sheets defined 33.8% alpha, 14.3% beta 54 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 8.75 Creating SS restraints... Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 159 through 177 removed outlier: 4.046A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.680A pdb=" N VAL A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 473 through 480 removed outlier: 4.193A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 671 through 693 removed outlier: 3.728A pdb=" N TYR A 689 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 693 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 730 Proline residue: A 720 - end of helix Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 219 through 231 removed outlier: 5.381A pdb=" N ASP C 223 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.676A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP C 343 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.893A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 414' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 447 through 457 removed outlier: 4.116A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 517 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 612 through 628 removed outlier: 3.725A pdb=" N LEU C 615 " --> pdb=" O PRO C 612 " (cutoff:3.500A) Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 745 through 756 Processing helix chain 'C' and resid 760 through 765 Processing helix chain 'C' and resid 792 through 804 removed outlier: 4.803A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 799 " --> pdb=" O ILE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 852 Proline residue: C 840 - end of helix removed outlier: 4.115A pdb=" N LYS C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 882 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 908 through 911 No H-bonds generated for 'chain 'C' and resid 908 through 911' Processing helix chain 'C' and resid 914 through 922 Processing helix chain 'C' and resid 959 through 974 removed outlier: 3.927A pdb=" N ARG C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 997 Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'f' and resid 15 through 21 Processing helix chain 'f' and resid 75 through 77 No H-bonds generated for 'chain 'f' and resid 75 through 77' Processing helix chain 'x' and resid 202 through 217 Processing helix chain 'd' and resid 6 through 14 Processing helix chain 'h' and resid 3 through 9 Processing helix chain 'h' and resid 103 through 107 Processing helix chain 'j' and resid 16 through 28 Processing helix chain 'j' and resid 32 through 40 Processing sheet with id= A, first strand: chain 'A' and resid 300 through 302 Processing sheet with id= B, first strand: chain 'C' and resid 320 through 322 removed outlier: 8.318A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL C 136 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN C 211 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C 138 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 213 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY C 140 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.659A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.540A pdb=" N TRP C 483 " --> pdb=" O VAL C 476 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 492 through 494 Processing sheet with id= F, first strand: chain 'C' and resid 603 through 607 removed outlier: 3.510A pdb=" N ILE C 633 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= H, first strand: chain 'C' and resid 774 through 778 removed outlier: 6.729A pdb=" N VAL C 816 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASP C 777 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR C 818 " --> pdb=" O ASP C 777 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 905 through 907 Processing sheet with id= J, first strand: chain 'C' and resid 867 through 869 Processing sheet with id= K, first strand: chain 'b' and resid 77 through 83 removed outlier: 6.288A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= M, first strand: chain 'e' and resid 58 through 61 removed outlier: 3.559A pdb=" N GLN e 34 " --> pdb=" O LEU e 31 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU e 31 " --> pdb=" O GLN e 34 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY e 36 " --> pdb=" O ILE e 29 " (cutoff:3.500A) removed outlier: 11.456A pdb=" N ILE e 29 " --> pdb=" O GLY e 36 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N ARG e 38 " --> pdb=" O VAL e 27 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL e 27 " --> pdb=" O ARG e 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'e' and resid 52 through 54 removed outlier: 3.861A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'f' and resid 37 through 39 removed outlier: 7.099A pdb=" N GLU f 58 " --> pdb=" O THR f 67 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR f 67 " --> pdb=" O GLU f 58 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'f' and resid 71 through 73 removed outlier: 3.651A pdb=" N GLN f 52 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER f 44 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'f' and resid 28 through 31 removed outlier: 4.008A pdb=" N TYR f 80 " --> pdb=" O LYS f 30 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'g' and resid 23 through 25 Processing sheet with id= S, first strand: chain 'g' and resid 60 through 63 removed outlier: 6.056A pdb=" N ASP g 41 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU g 29 " --> pdb=" O ASP g 41 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'd' and resid 69 through 73 removed outlier: 6.936A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'd' and resid 47 through 50 Processing sheet with id= V, first strand: chain 'h' and resid 80 through 82 removed outlier: 3.712A pdb=" N GLU h 13 " --> pdb=" O LEU h 29 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'h' and resid 84 through 87 removed outlier: 6.495A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'j' and resid 87 through 91 removed outlier: 3.592A pdb=" N ARG j 89 " --> pdb=" O GLU j 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'j' and resid 67 through 70 576 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2709 1.32 - 1.44: 6064 1.44 - 1.57: 10660 1.57 - 1.69: 341 1.69 - 1.82: 96 Bond restraints: 19870 Sorted by residual: bond pdb=" CA TYR A 403 " pdb=" C TYR A 403 " ideal model delta sigma weight residual 1.524 1.585 -0.060 8.80e-03 1.29e+04 4.70e+01 bond pdb=" CA ILE A 719 " pdb=" CB ILE A 719 " ideal model delta sigma weight residual 1.537 1.560 -0.023 5.00e-03 4.00e+04 2.10e+01 bond pdb=" N ASN A 404 " pdb=" CA ASN A 404 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.29e-02 6.01e+03 1.87e+01 bond pdb=" C LEU A 631 " pdb=" O LEU A 631 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C5 GTP C1101 " pdb=" C6 GTP C1101 " ideal model delta sigma weight residual 1.390 1.468 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 19865 not shown) Histogram of bond angle deviations from ideal: 98.56 - 106.07: 1363 106.07 - 113.58: 10930 113.58 - 121.08: 9104 121.08 - 128.59: 6072 128.59 - 136.10: 319 Bond angle restraints: 27788 Sorted by residual: angle pdb=" N ASN C 259 " pdb=" CA ASN C 259 " pdb=" C ASN C 259 " ideal model delta sigma weight residual 111.14 121.27 -10.13 1.08e+00 8.57e-01 8.79e+01 angle pdb=" C GLU C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.89 129.10 -9.21 1.02e+00 9.61e-01 8.16e+01 angle pdb=" O ILE A 719 " pdb=" C ILE A 719 " pdb=" N PRO A 720 " ideal model delta sigma weight residual 120.42 126.03 -5.61 6.40e-01 2.44e+00 7.68e+01 angle pdb=" C4' C U 95 " pdb=" C3' C U 95 " pdb=" O3' C U 95 " ideal model delta sigma weight residual 109.40 122.45 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" N ILE A 719 " pdb=" CA ILE A 719 " pdb=" CB ILE A 719 " ideal model delta sigma weight residual 110.52 115.93 -5.41 6.70e-01 2.23e+00 6.52e+01 ... (remaining 27783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 11310 35.27 - 70.55: 749 70.55 - 105.82: 69 105.82 - 141.10: 15 141.10 - 176.37: 11 Dihedral angle restraints: 12154 sinusoidal: 6234 harmonic: 5920 Sorted by residual: dihedral pdb=" CA ASN A 553 " pdb=" C ASN A 553 " pdb=" N THR A 554 " pdb=" CA THR A 554 " ideal model delta harmonic sigma weight residual 180.00 111.89 68.11 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N GLU A 465 " pdb=" CA GLU A 465 " ideal model delta harmonic sigma weight residual 180.00 124.34 55.66 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA PRO A 460 " pdb=" C PRO A 460 " pdb=" N LEU A 461 " pdb=" CA LEU A 461 " ideal model delta harmonic sigma weight residual -180.00 -129.76 -50.24 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 12151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2758 0.124 - 0.248: 543 0.248 - 0.373: 59 0.373 - 0.497: 14 0.497 - 0.621: 1 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C3' G U 129 " pdb=" C4' G U 129 " pdb=" O3' G U 129 " pdb=" C2' G U 129 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C3' G U 114 " pdb=" C4' G U 114 " pdb=" O3' G U 114 " pdb=" C2' G U 114 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA PHE A 506 " pdb=" N PHE A 506 " pdb=" C PHE A 506 " pdb=" CB PHE A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3372 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 839 " -0.095 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO C 840 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO C 840 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 840 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C U 108 " 0.006 2.00e-02 2.50e+03 2.93e-02 1.93e+01 pdb=" N1 C U 108 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C U 108 " 0.009 2.00e-02 2.50e+03 pdb=" O2 C U 108 " 0.029 2.00e-02 2.50e+03 pdb=" N3 C U 108 " -0.074 2.00e-02 2.50e+03 pdb=" C4 C U 108 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C U 108 " 0.033 2.00e-02 2.50e+03 pdb=" C5 C U 108 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C U 108 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 87 " -0.005 2.00e-02 2.50e+03 2.30e-02 1.59e+01 pdb=" N9 G U 87 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G U 87 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G U 87 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G U 87 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G U 87 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G U 87 " -0.046 2.00e-02 2.50e+03 pdb=" N1 G U 87 " 0.058 2.00e-02 2.50e+03 pdb=" C2 G U 87 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U 87 " -0.025 2.00e-02 2.50e+03 pdb=" N3 G U 87 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G U 87 " -0.003 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 91 2.56 - 3.15: 15059 3.15 - 3.73: 32733 3.73 - 4.32: 42764 4.32 - 4.90: 68323 Nonbonded interactions: 158970 Sorted by model distance: nonbonded pdb=" O2' U U 74 " pdb=" OP2 U U 76 " model vdw 1.976 2.440 nonbonded pdb=" CD1 LEU A 139 " pdb=" CD2 TYR A 193 " model vdw 2.154 3.760 nonbonded pdb=" N GLU A 467 " pdb=" OE1 GLU A 467 " model vdw 2.215 2.520 nonbonded pdb=" O2' C U 12 " pdb=" O4' A U 13 " model vdw 2.229 2.440 nonbonded pdb=" OP2 U U 33 " pdb=" OG1 THR A 296 " model vdw 2.264 2.440 ... (remaining 158965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.710 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 60.650 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 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 : 0.008 0.078 19870 Z= 0.517 Angle : 1.490 13.051 27788 Z= 1.027 Chirality : 0.099 0.621 3375 Planarity : 0.008 0.143 2884 Dihedral : 22.022 176.373 8312 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 1.83 % Allowed : 9.97 % Favored : 88.20 % Rotamer: Outliers : 6.60 % Allowed : 11.19 % Favored : 82.21 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.94 % Twisted General : 0.48 % 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: -2.90 (0.16), residues: 1966 helix: 0.44 (0.16), residues: 707 sheet: -3.28 (0.23), residues: 291 loop : -3.44 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP C 933 HIS 0.011 0.002 HIS A 636 PHE 0.032 0.003 PHE A 201 TYR 0.029 0.003 TYR C 354 ARG 0.006 0.001 ARG C 883 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 548 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6731 (mmm) cc_final: 0.6440 (mpp) REVERT: A 168 LEU cc_start: 0.8297 (tp) cc_final: 0.7783 (tp) REVERT: A 172 ILE cc_start: 0.8771 (mt) cc_final: 0.8470 (mt) REVERT: A 199 ILE cc_start: 0.7803 (tp) cc_final: 0.7556 (mp) REVERT: A 278 ASP cc_start: 0.9658 (m-30) cc_final: 0.9231 (t0) REVERT: A 284 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5846 (tpp80) REVERT: A 364 TYR cc_start: 0.2028 (OUTLIER) cc_final: 0.1804 (m-80) REVERT: A 374 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 375 PHE cc_start: 0.8330 (m-80) cc_final: 0.8084 (m-80) REVERT: A 417 TYR cc_start: 0.1475 (t80) cc_final: 0.0715 (t80) REVERT: A 533 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 572 CYS cc_start: 0.8369 (m) cc_final: 0.7714 (m) REVERT: A 635 THR cc_start: 0.8901 (p) cc_final: 0.8658 (m) REVERT: A 643 ASN cc_start: 0.9203 (m-40) cc_final: 0.8725 (p0) REVERT: A 689 TYR cc_start: 0.7975 (t80) cc_final: 0.7738 (t80) REVERT: C 113 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7964 (mt) REVERT: C 193 LEU cc_start: 0.8373 (tp) cc_final: 0.8129 (tp) REVERT: C 194 ASN cc_start: 0.7076 (m-40) cc_final: 0.6770 (m110) REVERT: C 196 SER cc_start: 0.7722 (p) cc_final: 0.7391 (p) REVERT: C 264 CYS cc_start: 0.7247 (m) cc_final: 0.6394 (m) REVERT: C 387 TYR cc_start: 0.8444 (m-80) cc_final: 0.7809 (m-80) REVERT: C 431 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: C 442 CYS cc_start: 0.6445 (t) cc_final: 0.6231 (m) REVERT: C 538 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8530 (tp30) REVERT: C 596 ASP cc_start: 0.7955 (m-30) cc_final: 0.7724 (t0) REVERT: C 675 THR cc_start: 0.7996 (p) cc_final: 0.7796 (t) REVERT: C 834 MET cc_start: 0.8752 (mmm) cc_final: 0.8532 (ptt) REVERT: C 842 MET cc_start: 0.9158 (mmm) cc_final: 0.8771 (tpp) REVERT: C 889 TYR cc_start: 0.8078 (m-80) cc_final: 0.7869 (m-10) REVERT: C 908 VAL cc_start: 0.7457 (t) cc_final: 0.7219 (t) REVERT: b 50 GLU cc_start: 0.8254 (tt0) cc_final: 0.8013 (tt0) REVERT: b 78 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8034 (tm-30) REVERT: b 100 LYS cc_start: 0.8756 (pttt) cc_final: 0.8511 (mmtt) REVERT: e 47 ASP cc_start: 0.8299 (t70) cc_final: 0.8072 (t70) REVERT: e 77 LEU cc_start: 0.6906 (tt) cc_final: 0.6474 (tp) REVERT: f 18 PHE cc_start: 0.8885 (t80) cc_final: 0.8683 (t80) REVERT: f 49 PHE cc_start: 0.9288 (m-80) cc_final: 0.8853 (m-80) REVERT: f 53 LEU cc_start: 0.9049 (mp) cc_final: 0.8770 (tp) REVERT: f 75 CYS cc_start: 0.8537 (p) cc_final: 0.8293 (p) REVERT: f 77 ASN cc_start: 0.7660 (m-40) cc_final: 0.7148 (m-40) REVERT: g 4 THR cc_start: 0.8200 (p) cc_final: 0.7975 (t) REVERT: g 25 VAL cc_start: 0.5439 (t) cc_final: 0.4694 (t) REVERT: g 30 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7652 (tpt90) REVERT: g 33 ASP cc_start: 0.7013 (p0) cc_final: 0.6734 (p0) REVERT: g 36 LEU cc_start: 0.9148 (tp) cc_final: 0.8825 (tt) REVERT: g 45 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6615 (mp0) REVERT: g 66 ASN cc_start: 0.8662 (t0) cc_final: 0.8219 (m-40) REVERT: g 67 SER cc_start: 0.8758 (p) cc_final: 0.8481 (p) REVERT: d 23 LEU cc_start: 0.8587 (mt) cc_final: 0.8387 (mp) REVERT: d 34 VAL cc_start: 0.7720 (t) cc_final: 0.7415 (t) REVERT: d 41 ASN cc_start: 0.6866 (m110) cc_final: 0.6227 (m-40) REVERT: d 60 ASP cc_start: 0.8931 (m-30) cc_final: 0.8683 (p0) REVERT: d 62 ILE cc_start: 0.6793 (tt) cc_final: 0.6562 (tp) REVERT: d 63 PHE cc_start: 0.7322 (t80) cc_final: 0.7060 (t80) REVERT: d 70 LYS cc_start: 0.8913 (tttm) cc_final: 0.8455 (ttmm) REVERT: h 18 GLU cc_start: 0.9005 (tt0) cc_final: 0.8719 (tm-30) REVERT: h 20 LYS cc_start: 0.2823 (OUTLIER) cc_final: 0.2479 (tptt) REVERT: h 39 ILE cc_start: 0.9255 (mt) cc_final: 0.8801 (tt) REVERT: h 90 ASN cc_start: 0.8001 (p0) cc_final: 0.7545 (p0) REVERT: h 94 GLN cc_start: 0.9096 (mt0) cc_final: 0.8875 (mt0) REVERT: j 35 ASN cc_start: 0.9431 (t0) cc_final: 0.8977 (m110) REVERT: j 62 ASP cc_start: 0.8001 (p0) cc_final: 0.7434 (p0) REVERT: j 90 PHE cc_start: 0.9339 (m-80) cc_final: 0.9106 (t80) REVERT: j 92 SER cc_start: 0.9159 (m) cc_final: 0.8751 (p) REVERT: j 93 LYS cc_start: 0.7713 (mttp) cc_final: 0.7420 (mtmt) REVERT: j 101 VAL cc_start: 0.8295 (t) cc_final: 0.7882 (p) REVERT: j 106 LYS cc_start: 0.9212 (tttt) cc_final: 0.8929 (tptt) outliers start: 108 outliers final: 34 residues processed: 626 average time/residue: 0.3249 time to fit residues: 303.0818 Evaluate side-chains 413 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 373 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 770 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain h residue 20 LYS Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain j residue 24 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 194 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 216 GLN A 254 HIS A 310 ASN A 344 ASN A 392 ASN A 412 GLN A 528 ASN A 559 GLN A 576 HIS A 617 ASN A 654 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN C 260 ASN C 289 ASN C 418 GLN C 423 HIS C 431 GLN C 560 GLN C 776 ASN b 14 ASN e 23 GLN ** f 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 94 GLN j 28 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19870 Z= 0.257 Angle : 0.881 14.822 27788 Z= 0.449 Chirality : 0.052 0.369 3375 Planarity : 0.006 0.094 2884 Dihedral : 23.301 178.740 4805 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 5.32 % Allowed : 18.83 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.50 (0.19), residues: 1966 helix: 1.76 (0.21), residues: 705 sheet: -2.50 (0.25), residues: 302 loop : -2.75 (0.17), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 933 HIS 0.009 0.001 HIS j 28 PHE 0.026 0.002 PHE C 212 TYR 0.034 0.002 TYR C 791 ARG 0.008 0.001 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 409 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6397 (mmm) cc_final: 0.5917 (mpp) REVERT: A 168 LEU cc_start: 0.8207 (tp) cc_final: 0.7951 (tp) REVERT: A 278 ASP cc_start: 0.9666 (m-30) cc_final: 0.9277 (t0) REVERT: A 417 TYR cc_start: 0.2502 (t80) cc_final: 0.1514 (t80) REVERT: C 113 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7188 (mt) REVERT: C 209 MET cc_start: 0.7110 (ttp) cc_final: 0.6728 (ttp) REVERT: C 264 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6389 (m) REVERT: C 387 TYR cc_start: 0.8377 (m-80) cc_final: 0.7676 (m-80) REVERT: C 431 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7301 (pp30) REVERT: C 432 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: C 596 ASP cc_start: 0.8009 (m-30) cc_final: 0.7745 (t0) REVERT: C 629 TYR cc_start: 0.6537 (m-80) cc_final: 0.6327 (m-80) REVERT: C 652 MET cc_start: 0.8410 (mmm) cc_final: 0.7987 (mmm) REVERT: C 842 MET cc_start: 0.9160 (mmm) cc_final: 0.8799 (tpp) REVERT: C 856 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.6874 (tp) REVERT: C 882 LYS cc_start: 0.9173 (mttt) cc_final: 0.8905 (tmtt) REVERT: C 933 TRP cc_start: 0.7731 (OUTLIER) cc_final: 0.7158 (m-90) REVERT: C 971 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6833 (mtm-85) REVERT: b 4 ILE cc_start: 0.5584 (mm) cc_final: 0.5306 (tp) REVERT: b 5 GLN cc_start: 0.8871 (pm20) cc_final: 0.8597 (tp40) REVERT: b 48 CYS cc_start: 0.9168 (t) cc_final: 0.8846 (p) REVERT: b 50 GLU cc_start: 0.8335 (tt0) cc_final: 0.8029 (tt0) REVERT: b 94 SER cc_start: 0.8187 (p) cc_final: 0.7985 (m) REVERT: b 100 LYS cc_start: 0.8818 (pttt) cc_final: 0.8597 (mmmt) REVERT: e 81 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8175 (tt) REVERT: f 53 LEU cc_start: 0.8951 (mp) cc_final: 0.8686 (mt) REVERT: f 77 ASN cc_start: 0.7656 (m-40) cc_final: 0.7421 (m-40) REVERT: f 80 TYR cc_start: 0.8159 (p90) cc_final: 0.7803 (p90) REVERT: g 25 VAL cc_start: 0.5516 (t) cc_final: 0.5219 (t) REVERT: g 66 ASN cc_start: 0.8717 (t0) cc_final: 0.8269 (t0) REVERT: d 70 LYS cc_start: 0.8874 (tttm) cc_final: 0.8595 (ttmt) REVERT: h 90 ASN cc_start: 0.7995 (p0) cc_final: 0.7754 (p0) REVERT: h 96 ILE cc_start: 0.8674 (mm) cc_final: 0.8266 (mm) REVERT: j 90 PHE cc_start: 0.9382 (m-80) cc_final: 0.9136 (t80) REVERT: j 101 VAL cc_start: 0.8178 (t) cc_final: 0.7976 (p) REVERT: j 106 LYS cc_start: 0.8800 (tttt) cc_final: 0.8567 (tptt) outliers start: 87 outliers final: 38 residues processed: 465 average time/residue: 0.2850 time to fit residues: 203.7223 Evaluate side-chains 379 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 333 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 917 ASP Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 971 ARG Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 34 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 343 ASN A 497 GLN A 713 ASN C 143 HIS C 290 HIS C 355 HIS C 554 HIS e 23 GLN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 HIS d 41 ASN ** h 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 19870 Z= 0.500 Angle : 0.916 14.390 27788 Z= 0.466 Chirality : 0.052 0.341 3375 Planarity : 0.006 0.072 2884 Dihedral : 23.192 178.555 4764 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.55 % Favored : 91.15 % Rotamer: Outliers : 8.44 % Allowed : 18.70 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.62 (0.18), residues: 1966 helix: 1.23 (0.20), residues: 684 sheet: -2.15 (0.25), residues: 321 loop : -2.51 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 933 HIS 0.006 0.002 HIS A 254 PHE 0.042 0.003 PHE A 484 TYR 0.029 0.003 TYR A 298 ARG 0.009 0.001 ARG C 964 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 337 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.9390 (m-30) cc_final: 0.9154 (t0) REVERT: A 298 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6213 (t80) REVERT: A 364 TYR cc_start: 0.1682 (OUTLIER) cc_final: 0.1386 (m-80) REVERT: C 113 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7625 (mt) REVERT: C 142 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8469 (tm) REVERT: C 431 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: C 540 GLU cc_start: 0.8780 (mp0) cc_final: 0.8560 (mp0) REVERT: C 596 ASP cc_start: 0.8104 (m-30) cc_final: 0.7823 (t0) REVERT: C 614 GLU cc_start: 0.8734 (mp0) cc_final: 0.8433 (mp0) REVERT: C 641 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8242 (pt0) REVERT: C 834 MET cc_start: 0.8688 (mmm) cc_final: 0.8440 (ptt) REVERT: C 842 MET cc_start: 0.9174 (mmm) cc_final: 0.8858 (tpp) REVERT: C 856 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7099 (tp) REVERT: C 981 PHE cc_start: 0.8079 (p90) cc_final: 0.7397 (t80) REVERT: b 52 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8201 (ttm110) REVERT: b 94 SER cc_start: 0.8256 (p) cc_final: 0.8025 (m) REVERT: e 80 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7004 (mm) REVERT: e 81 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8559 (tt) REVERT: f 77 ASN cc_start: 0.7715 (m-40) cc_final: 0.7330 (m-40) REVERT: f 80 TYR cc_start: 0.8179 (p90) cc_final: 0.7919 (p90) REVERT: g 39 VAL cc_start: 0.8004 (t) cc_final: 0.7674 (m) REVERT: j 38 MET cc_start: 0.8700 (ttp) cc_final: 0.8397 (tpt) REVERT: j 90 PHE cc_start: 0.9348 (m-80) cc_final: 0.9064 (t80) REVERT: j 101 VAL cc_start: 0.8081 (t) cc_final: 0.7827 (p) outliers start: 138 outliers final: 83 residues processed: 424 average time/residue: 0.2807 time to fit residues: 188.5890 Evaluate side-chains 386 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 295 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 796 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 80 ILE Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 7 LEU Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 71 ASN Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 713 ASN C 451 ASN C 869 HIS e 23 GLN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19870 Z= 0.243 Angle : 0.797 14.614 27788 Z= 0.400 Chirality : 0.048 0.316 3375 Planarity : 0.005 0.063 2884 Dihedral : 22.971 177.075 4762 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.51 % Favored : 93.18 % Rotamer: Outliers : 6.72 % Allowed : 23.47 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.48 (0.19), residues: 1966 helix: 1.16 (0.21), residues: 686 sheet: -1.88 (0.25), residues: 341 loop : -2.35 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 933 HIS 0.007 0.001 HIS A 138 PHE 0.026 0.002 PHE d 63 TYR 0.020 0.002 TYR C 791 ARG 0.004 0.001 ARG j 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 362 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6802 (mmm) cc_final: 0.6413 (mpp) REVERT: A 278 ASP cc_start: 0.9380 (m-30) cc_final: 0.9165 (t0) REVERT: A 493 MET cc_start: 0.6830 (mmt) cc_final: 0.6555 (mpp) REVERT: C 113 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7543 (mt) REVERT: C 202 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6107 (m-30) REVERT: C 431 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7289 (pp30) REVERT: C 499 VAL cc_start: 0.8687 (t) cc_final: 0.8359 (p) REVERT: C 540 GLU cc_start: 0.8754 (mp0) cc_final: 0.8537 (mp0) REVERT: C 596 ASP cc_start: 0.8129 (m-30) cc_final: 0.7872 (t0) REVERT: C 608 GLN cc_start: 0.7534 (mt0) cc_final: 0.7301 (mp10) REVERT: C 614 GLU cc_start: 0.8543 (mp0) cc_final: 0.8223 (mp0) REVERT: C 816 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7552 (t) REVERT: C 834 MET cc_start: 0.8739 (mmm) cc_final: 0.8401 (ptt) REVERT: C 842 MET cc_start: 0.9221 (mmm) cc_final: 0.8887 (tpp) REVERT: C 856 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7206 (tp) REVERT: C 931 TYR cc_start: 0.6704 (p90) cc_final: 0.6424 (p90) REVERT: C 933 TRP cc_start: 0.7760 (m100) cc_final: 0.7435 (m100) REVERT: C 981 PHE cc_start: 0.8078 (p90) cc_final: 0.7397 (t80) REVERT: b 94 SER cc_start: 0.8220 (p) cc_final: 0.7947 (m) REVERT: f 77 ASN cc_start: 0.7732 (m-40) cc_final: 0.7350 (m-40) REVERT: g 61 THR cc_start: 0.8523 (m) cc_final: 0.8321 (p) REVERT: h 30 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6702 (mt0) REVERT: h 36 MET cc_start: 0.8967 (mtm) cc_final: 0.8765 (mpp) REVERT: j 24 PHE cc_start: 0.9525 (OUTLIER) cc_final: 0.9311 (p90) REVERT: j 101 VAL cc_start: 0.8032 (t) cc_final: 0.7821 (p) outliers start: 110 outliers final: 63 residues processed: 429 average time/residue: 0.2838 time to fit residues: 191.9487 Evaluate side-chains 374 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 304 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 18 PHE Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 51 ASN Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 71 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain j residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 176 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 259 ASN C 451 ASN f 54 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 GLN ** h 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19870 Z= 0.222 Angle : 0.772 14.594 27788 Z= 0.387 Chirality : 0.048 0.311 3375 Planarity : 0.005 0.059 2884 Dihedral : 22.687 177.642 4758 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.68 % Rotamer: Outliers : 6.05 % Allowed : 25.61 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.34 (0.19), residues: 1966 helix: 1.03 (0.21), residues: 685 sheet: -1.61 (0.26), residues: 330 loop : -2.13 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 933 HIS 0.006 0.001 HIS j 28 PHE 0.030 0.002 PHE d 63 TYR 0.019 0.001 TYR A 298 ARG 0.008 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 341 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7047 (mmm) cc_final: 0.6685 (mpp) REVERT: A 278 ASP cc_start: 0.9311 (m-30) cc_final: 0.9104 (t0) REVERT: A 364 TYR cc_start: 0.1719 (OUTLIER) cc_final: 0.1347 (m-80) REVERT: A 493 MET cc_start: 0.6844 (mmt) cc_final: 0.6494 (mpp) REVERT: C 113 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7402 (mt) REVERT: C 431 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7260 (pp30) REVERT: C 484 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7004 (p) REVERT: C 499 VAL cc_start: 0.8597 (t) cc_final: 0.8374 (p) REVERT: C 540 GLU cc_start: 0.8767 (mp0) cc_final: 0.8532 (mp0) REVERT: C 596 ASP cc_start: 0.8136 (m-30) cc_final: 0.7883 (t0) REVERT: C 614 GLU cc_start: 0.8648 (mp0) cc_final: 0.8390 (mp0) REVERT: C 834 MET cc_start: 0.8735 (mmm) cc_final: 0.8330 (ptt) REVERT: C 842 MET cc_start: 0.9243 (mmm) cc_final: 0.8914 (tpp) REVERT: C 856 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7065 (tp) REVERT: C 869 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7278 (m90) REVERT: C 931 TYR cc_start: 0.6819 (p90) cc_final: 0.6587 (p90) REVERT: C 981 PHE cc_start: 0.8077 (p90) cc_final: 0.7395 (t80) REVERT: b 94 SER cc_start: 0.8212 (p) cc_final: 0.7956 (m) REVERT: f 77 ASN cc_start: 0.7694 (m-40) cc_final: 0.7376 (m-40) REVERT: g 11 MET cc_start: 0.7839 (tpp) cc_final: 0.7604 (mmm) REVERT: h 30 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6025 (mm-40) REVERT: j 31 MET cc_start: 0.9392 (tpp) cc_final: 0.9007 (tpt) REVERT: j 51 ASN cc_start: 0.8059 (p0) cc_final: 0.7853 (p0) outliers start: 99 outliers final: 60 residues processed: 403 average time/residue: 0.2707 time to fit residues: 173.0371 Evaluate side-chains 376 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 309 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 451 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19870 Z= 0.213 Angle : 0.761 14.631 27788 Z= 0.378 Chirality : 0.047 0.389 3375 Planarity : 0.005 0.059 2884 Dihedral : 22.457 177.447 4755 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.68 % Rotamer: Outliers : 5.87 % Allowed : 26.04 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.27 (0.19), residues: 1966 helix: 1.04 (0.21), residues: 685 sheet: -1.54 (0.26), residues: 356 loop : -2.05 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 26 HIS 0.006 0.001 HIS C 455 PHE 0.023 0.002 PHE d 63 TYR 0.023 0.002 TYR f 80 ARG 0.009 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 331 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7243 (mmm) cc_final: 0.6835 (mpp) REVERT: A 273 ASP cc_start: 0.9137 (m-30) cc_final: 0.8605 (p0) REVERT: A 298 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 364 TYR cc_start: 0.1849 (OUTLIER) cc_final: 0.1398 (m-80) REVERT: A 493 MET cc_start: 0.6818 (mmt) cc_final: 0.6460 (mpp) REVERT: A 559 GLN cc_start: 0.7622 (mp-120) cc_final: 0.7354 (mm-40) REVERT: C 113 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7496 (mt) REVERT: C 431 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: C 484 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.6973 (p) REVERT: C 499 VAL cc_start: 0.8739 (t) cc_final: 0.8522 (p) REVERT: C 540 GLU cc_start: 0.8769 (mp0) cc_final: 0.8535 (mp0) REVERT: C 596 ASP cc_start: 0.8144 (m-30) cc_final: 0.7898 (t0) REVERT: C 614 GLU cc_start: 0.8530 (mp0) cc_final: 0.8261 (mp0) REVERT: C 834 MET cc_start: 0.8797 (mmm) cc_final: 0.8487 (ptt) REVERT: C 842 MET cc_start: 0.9241 (mmm) cc_final: 0.8848 (tpt) REVERT: C 856 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7338 (tp) REVERT: C 869 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7287 (m90) REVERT: b 94 SER cc_start: 0.8212 (p) cc_final: 0.7960 (m) REVERT: e 21 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7289 (mt) REVERT: f 80 TYR cc_start: 0.8824 (p90) cc_final: 0.8390 (p90) REVERT: h 30 GLN cc_start: 0.6420 (OUTLIER) cc_final: 0.6095 (mm-40) REVERT: h 35 GLN cc_start: 0.8263 (mt0) cc_final: 0.7970 (pt0) REVERT: j 31 MET cc_start: 0.9401 (tpp) cc_final: 0.8978 (tpt) outliers start: 96 outliers final: 58 residues processed: 396 average time/residue: 0.2800 time to fit residues: 175.0734 Evaluate side-chains 370 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 303 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 971 ARG Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 53 LYS Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 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 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19870 Z= 0.227 Angle : 0.773 14.706 27788 Z= 0.383 Chirality : 0.048 0.330 3375 Planarity : 0.005 0.059 2884 Dihedral : 22.313 178.093 4751 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.17 % Favored : 92.57 % Rotamer: Outliers : 6.11 % Allowed : 25.79 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.14 (0.19), residues: 1966 helix: 0.98 (0.21), residues: 688 sheet: -1.15 (0.28), residues: 316 loop : -1.97 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 933 HIS 0.004 0.001 HIS A 138 PHE 0.018 0.002 PHE d 63 TYR 0.022 0.002 TYR A 391 ARG 0.010 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 319 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6922 (mmm) cc_final: 0.6516 (mpp) REVERT: A 298 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6318 (t80) REVERT: A 364 TYR cc_start: 0.1907 (OUTLIER) cc_final: 0.1469 (m-80) REVERT: A 493 MET cc_start: 0.7206 (mmt) cc_final: 0.6888 (mpp) REVERT: A 529 TYR cc_start: 0.8035 (t80) cc_final: 0.7816 (t80) REVERT: A 559 GLN cc_start: 0.7620 (mp-120) cc_final: 0.7418 (mm-40) REVERT: A 701 CYS cc_start: 0.4934 (t) cc_final: 0.4681 (t) REVERT: C 222 MET cc_start: 0.7474 (tpp) cc_final: 0.7107 (tpp) REVERT: C 431 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7227 (pp30) REVERT: C 484 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.6997 (p) REVERT: C 499 VAL cc_start: 0.8715 (t) cc_final: 0.8501 (p) REVERT: C 540 GLU cc_start: 0.8866 (mp0) cc_final: 0.8630 (mp0) REVERT: C 596 ASP cc_start: 0.8140 (m-30) cc_final: 0.7882 (t0) REVERT: C 614 GLU cc_start: 0.8653 (mp0) cc_final: 0.8413 (mp0) REVERT: C 641 GLU cc_start: 0.8097 (pt0) cc_final: 0.7696 (pp20) REVERT: C 834 MET cc_start: 0.8948 (mmm) cc_final: 0.8648 (ptt) REVERT: C 842 MET cc_start: 0.9251 (mmm) cc_final: 0.8864 (tpt) REVERT: C 856 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7349 (tp) REVERT: C 869 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7308 (m90) REVERT: b 85 THR cc_start: 0.8573 (p) cc_final: 0.8373 (p) REVERT: b 94 SER cc_start: 0.8227 (p) cc_final: 0.7983 (m) REVERT: e 21 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7358 (mt) REVERT: e 51 ASN cc_start: 0.8556 (m-40) cc_final: 0.7840 (p0) REVERT: f 80 TYR cc_start: 0.8809 (p90) cc_final: 0.8401 (p90) REVERT: d 35 GLU cc_start: 0.6401 (tm-30) cc_final: 0.5917 (tm-30) REVERT: h 36 MET cc_start: 0.8865 (mpp) cc_final: 0.8624 (mtm) REVERT: h 77 ASP cc_start: 0.5082 (t70) cc_final: 0.4818 (t70) REVERT: j 31 MET cc_start: 0.9491 (tpp) cc_final: 0.9032 (tpp) outliers start: 100 outliers final: 68 residues processed: 381 average time/residue: 0.2725 time to fit residues: 165.3526 Evaluate side-chains 379 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 304 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 971 ARG Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 71 ASN Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19870 Z= 0.215 Angle : 0.769 14.929 27788 Z= 0.380 Chirality : 0.047 0.392 3375 Planarity : 0.005 0.058 2884 Dihedral : 22.154 178.182 4749 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.82 % Favored : 92.93 % Rotamer: Outliers : 4.95 % Allowed : 27.57 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.05 (0.19), residues: 1966 helix: 0.93 (0.21), residues: 691 sheet: -1.06 (0.28), residues: 335 loop : -1.83 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 933 HIS 0.004 0.001 HIS A 138 PHE 0.031 0.001 PHE C 446 TYR 0.022 0.002 TYR A 391 ARG 0.012 0.001 ARG f 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 334 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 364 TYR cc_start: 0.1653 (OUTLIER) cc_final: 0.1169 (m-80) REVERT: A 493 MET cc_start: 0.7232 (mmt) cc_final: 0.6856 (mpp) REVERT: A 559 GLN cc_start: 0.8066 (mp-120) cc_final: 0.7830 (mm-40) REVERT: C 197 THR cc_start: 0.7685 (p) cc_final: 0.7442 (p) REVERT: C 431 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: C 484 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7016 (p) REVERT: C 499 VAL cc_start: 0.8701 (t) cc_final: 0.8486 (p) REVERT: C 540 GLU cc_start: 0.8856 (mp0) cc_final: 0.8612 (mp0) REVERT: C 586 MET cc_start: 0.8646 (tmm) cc_final: 0.8396 (mtp) REVERT: C 596 ASP cc_start: 0.8202 (m-30) cc_final: 0.7981 (t0) REVERT: C 614 GLU cc_start: 0.8626 (mp0) cc_final: 0.8401 (mp0) REVERT: C 641 GLU cc_start: 0.8307 (pt0) cc_final: 0.8060 (pp20) REVERT: C 834 MET cc_start: 0.8935 (mmm) cc_final: 0.8669 (ptt) REVERT: C 842 MET cc_start: 0.9256 (mmm) cc_final: 0.8939 (tpp) REVERT: C 856 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7469 (tp) REVERT: C 869 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7273 (m90) REVERT: C 931 TYR cc_start: 0.6279 (p90) cc_final: 0.5960 (p90) REVERT: b 18 TYR cc_start: 0.6366 (m-80) cc_final: 0.5870 (m-80) REVERT: b 94 SER cc_start: 0.8255 (p) cc_final: 0.7934 (m) REVERT: e 21 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7313 (mt) REVERT: f 80 TYR cc_start: 0.8821 (p90) cc_final: 0.8408 (p90) outliers start: 81 outliers final: 61 residues processed: 388 average time/residue: 0.2803 time to fit residues: 172.3774 Evaluate side-chains 380 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 312 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19870 Z= 0.251 Angle : 0.784 15.416 27788 Z= 0.386 Chirality : 0.046 0.368 3375 Planarity : 0.005 0.059 2884 Dihedral : 22.125 178.593 4749 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.32 % Rotamer: Outliers : 5.07 % Allowed : 28.12 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % 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: -1.03 (0.19), residues: 1966 helix: 0.96 (0.21), residues: 691 sheet: -1.20 (0.28), residues: 334 loop : -1.76 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 933 HIS 0.003 0.001 HIS C 355 PHE 0.030 0.002 PHE C 446 TYR 0.019 0.002 TYR A 556 ARG 0.012 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 316 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6533 (t80) REVERT: A 364 TYR cc_start: 0.1667 (OUTLIER) cc_final: 0.1222 (m-80) REVERT: A 493 MET cc_start: 0.7238 (mmt) cc_final: 0.6884 (mpp) REVERT: C 431 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: C 484 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7075 (p) REVERT: C 499 VAL cc_start: 0.8647 (t) cc_final: 0.8434 (p) REVERT: C 540 GLU cc_start: 0.8787 (mp0) cc_final: 0.8521 (mp0) REVERT: C 586 MET cc_start: 0.8654 (tmm) cc_final: 0.8402 (mtp) REVERT: C 596 ASP cc_start: 0.8181 (m-30) cc_final: 0.7964 (t0) REVERT: C 614 GLU cc_start: 0.8724 (mp0) cc_final: 0.8493 (mp0) REVERT: C 834 MET cc_start: 0.8933 (mmm) cc_final: 0.8676 (ptt) REVERT: C 842 MET cc_start: 0.9238 (mmm) cc_final: 0.8925 (tpp) REVERT: C 856 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7498 (tp) REVERT: C 869 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7298 (m90) REVERT: C 931 TYR cc_start: 0.6368 (p90) cc_final: 0.6019 (p90) REVERT: b 94 SER cc_start: 0.8325 (p) cc_final: 0.8058 (m) REVERT: e 21 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7395 (mt) REVERT: f 80 TYR cc_start: 0.8800 (p90) cc_final: 0.8401 (p90) outliers start: 83 outliers final: 67 residues processed: 371 average time/residue: 0.2598 time to fit residues: 153.8924 Evaluate side-chains 385 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 311 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 95 ILE Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 0.0470 chunk 141 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19870 Z= 0.225 Angle : 0.798 15.473 27788 Z= 0.389 Chirality : 0.047 0.391 3375 Planarity : 0.005 0.063 2884 Dihedral : 22.048 178.482 4746 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 4.52 % Allowed : 28.85 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.19), residues: 1966 helix: 0.94 (0.21), residues: 690 sheet: -1.11 (0.28), residues: 350 loop : -1.78 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 933 HIS 0.003 0.001 HIS A 576 PHE 0.030 0.001 PHE C 446 TYR 0.033 0.002 TYR A 529 ARG 0.012 0.001 ARG b 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 320 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6522 (t80) REVERT: A 364 TYR cc_start: 0.1654 (OUTLIER) cc_final: 0.1173 (m-80) REVERT: A 493 MET cc_start: 0.7236 (mmt) cc_final: 0.6874 (mpp) REVERT: C 197 THR cc_start: 0.7832 (p) cc_final: 0.7613 (p) REVERT: C 387 TYR cc_start: 0.8225 (m-80) cc_final: 0.7815 (m-80) REVERT: C 431 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7086 (pp30) REVERT: C 484 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7040 (p) REVERT: C 499 VAL cc_start: 0.8654 (t) cc_final: 0.8429 (p) REVERT: C 540 GLU cc_start: 0.8785 (mp0) cc_final: 0.8516 (mp0) REVERT: C 586 MET cc_start: 0.8663 (tmm) cc_final: 0.8420 (mtp) REVERT: C 596 ASP cc_start: 0.8182 (m-30) cc_final: 0.7973 (t0) REVERT: C 614 GLU cc_start: 0.8755 (mp0) cc_final: 0.8542 (mp0) REVERT: C 834 MET cc_start: 0.8944 (mmm) cc_final: 0.8704 (ptt) REVERT: C 842 MET cc_start: 0.9205 (mmm) cc_final: 0.8867 (tpp) REVERT: C 869 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7318 (m90) REVERT: C 931 TYR cc_start: 0.6354 (p90) cc_final: 0.5953 (p90) REVERT: b 28 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7807 (mmp80) REVERT: b 90 GLU cc_start: 0.7684 (tp30) cc_final: 0.7235 (mt-10) REVERT: b 94 SER cc_start: 0.8307 (p) cc_final: 0.8079 (m) REVERT: e 21 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7292 (mt) REVERT: f 80 TYR cc_start: 0.8886 (p90) cc_final: 0.8509 (p90) REVERT: j 57 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8239 (mmm-85) outliers start: 74 outliers final: 63 residues processed: 368 average time/residue: 0.3012 time to fit residues: 177.5297 Evaluate side-chains 380 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 311 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 431 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 883 ARG Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain h residue 12 ASN Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 95 ILE Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 109 ASP Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 170 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 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 = 0.3831 r_free = 0.3831 target = 0.090046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068343 restraints weight = 72327.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070201 restraints weight = 36657.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.071403 restraints weight = 23957.512| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19870 Z= 0.207 Angle : 0.777 15.458 27788 Z= 0.379 Chirality : 0.046 0.370 3375 Planarity : 0.005 0.060 2884 Dihedral : 21.954 178.775 4746 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.52 % Rotamer: Outliers : 4.40 % Allowed : 28.79 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.96 (0.19), residues: 1966 helix: 0.96 (0.21), residues: 689 sheet: -1.06 (0.28), residues: 318 loop : -1.71 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 933 HIS 0.008 0.001 HIS A 659 PHE 0.030 0.001 PHE C 446 TYR 0.022 0.001 TYR A 417 ARG 0.012 0.001 ARG b 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4329.03 seconds wall clock time: 81 minutes 26.55 seconds (4886.55 seconds total)