Starting phenix.real_space_refine (version: dev) on Fri Feb 24 19:59:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2023/8f4r_28857_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23675 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7865 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7898 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7881 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LLL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.19, per 1000 atoms: 0.56 Number of scatterers: 23675 At special positions: 0 Unit cell: (124.12, 114.49, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4429 8.00 N 3992 7.00 C 15122 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: 10.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 27 sheets defined 54.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.523A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.962A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.769A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.885A pdb=" N GLN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 358 Processing helix chain 'A' and resid 362 through 385 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 removed outlier: 4.160A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 439 through 458 Proline residue: A 455 - end of helix removed outlier: 4.144A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.554A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 511 through 535 Processing helix chain 'A' and resid 537 through 557 Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 643 through 655 Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.683A pdb=" N GLU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 741 through 751 Processing helix chain 'A' and resid 775 through 777 No H-bonds generated for 'chain 'A' and resid 775 through 777' Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 835 through 848 Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 870 through 890 Processing helix chain 'A' and resid 895 through 916 removed outlier: 3.830A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Proline residue: A 904 - end of helix removed outlier: 3.506A pdb=" N VAL A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 952 Processing helix chain 'A' and resid 957 through 987 removed outlier: 4.549A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 994 through 1029 removed outlier: 4.271A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.539A pdb=" N PHE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.056A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.627A pdb=" N GLN B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 316 removed outlier: 3.702A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.747A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 3.507A pdb=" N ILE B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 3.917A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.045A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 486 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 510 through 534 removed outlier: 3.775A pdb=" N TRP B 514 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE B 515 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 534 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 Processing helix chain 'B' and resid 583 through 599 Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.050A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 741 through 752 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.683A pdb=" N ILE B 784 " --> pdb=" O PRO B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 835 through 848 removed outlier: 3.571A pdb=" N LYS B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 890 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 895 through 917 removed outlier: 4.286A pdb=" N VAL B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Proline residue: B 904 - end of helix removed outlier: 3.986A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 953 removed outlier: 4.564A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 967 Processing helix chain 'B' and resid 969 through 987 Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 994 through 1013 removed outlier: 4.365A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1029 Proline residue: B1020 - end of helix Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.527A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.139A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 removed outlier: 4.549A pdb=" N TYR C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.843A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.569A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'C' and resid 402 through 422 removed outlier: 4.176A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 458 removed outlier: 5.757A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.988A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 495 removed outlier: 4.593A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 512 through 533 removed outlier: 4.242A pdb=" N ILE C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 557 Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 707 Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 741 through 751 Processing helix chain 'C' and resid 775 through 777 No H-bonds generated for 'chain 'C' and resid 775 through 777' Processing helix chain 'C' and resid 781 through 786 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 835 through 848 Processing helix chain 'C' and resid 860 through 866 Processing helix chain 'C' and resid 871 through 890 Processing helix chain 'C' and resid 895 through 916 removed outlier: 4.457A pdb=" N VAL C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Proline residue: C 904 - end of helix removed outlier: 3.998A pdb=" N GLY C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 953 removed outlier: 3.752A pdb=" N ILE C 943 " --> pdb=" O ASN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 987 removed outlier: 4.867A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Proline residue: C 971 - end of helix Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 994 through 1029 removed outlier: 4.314A pdb=" N GLY C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Proline residue: C1020 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.957A pdb=" N VAL A 291 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 139 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU A 289 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 141 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER A 287 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.162A pdb=" N VAL A 766 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N MET A 184 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 768 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 186 " --> pdb=" O LYS A 768 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 770 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A 188 " --> pdb=" O TYR A 770 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN A 772 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.731A pdb=" N ARG A 629 " --> pdb=" O MET A 606 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 608 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 627 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 610 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG A 625 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A 612 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 623 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 822 through 828 removed outlier: 4.294A pdb=" N ASP A 680 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 721 through 729 Processing sheet with id= G, first strand: chain 'A' and resid 788 through 790 Processing sheet with id= H, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.860A pdb=" N ILE A 234 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.798A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.540A pdb=" N TYR B 77 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.895A pdb=" N VAL B 291 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 139 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 289 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 141 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 287 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.386A pdb=" N TYR B 182 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.128A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 284 through 286 removed outlier: 4.251A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG B 629 " --> pdb=" O MET B 606 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 610 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 612 " --> pdb=" O VAL B 623 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 822 through 826 Processing sheet with id= P, first strand: chain 'B' and resid 721 through 729 Processing sheet with id= Q, first strand: chain 'B' and resid 788 through 790 Processing sheet with id= R, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.841A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= U, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.290A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 629 " --> pdb=" O MET C 606 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA C 610 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL C 612 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 623 " --> pdb=" O VAL C 612 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 822 through 826 Processing sheet with id= W, first strand: chain 'C' and resid 721 through 729 Processing sheet with id= X, first strand: chain 'C' and resid 759 through 762 Processing sheet with id= Y, first strand: chain 'C' and resid 788 through 790 Processing sheet with id= Z, first strand: chain 'C' and resid 321 through 328 removed outlier: 6.476A pdb=" N THR C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU C 328 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE C 137 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 291 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU C 289 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 141 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER C 287 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.657A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 3936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.74 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7775 1.34 - 1.46: 3862 1.46 - 1.57: 12240 1.57 - 1.69: 5 1.69 - 1.81: 252 Bond restraints: 24134 Sorted by residual: bond pdb=" C51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sigma weight residual 1.515 1.590 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C42 LLL B1101 " pdb=" C52 LLL B1101 " ideal model delta sigma weight residual 1.529 1.601 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA PHE A1030 " pdb=" C PHE A1030 " ideal model delta sigma weight residual 1.532 1.511 0.022 6.50e-03 2.37e+04 1.10e+01 bond pdb=" C32 LLL B1101 " pdb=" C42 LLL B1101 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C33 LLL B1101 " pdb=" C43 LLL B1101 " ideal model delta sigma weight residual 1.541 1.603 -0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 24129 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 690 106.65 - 113.49: 13429 113.49 - 120.33: 8414 120.33 - 127.17: 10049 127.17 - 134.00: 218 Bond angle restraints: 32800 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C LEU B 500 " pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " ideal model delta sigma weight residual 117.23 110.78 6.45 1.36e+00 5.41e-01 2.25e+01 angle pdb=" C ASN C 818 " pdb=" CA ASN C 818 " pdb=" CB ASN C 818 " ideal model delta sigma weight residual 116.54 111.21 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" C SER C 894 " pdb=" N VAL C 895 " pdb=" CA VAL C 895 " ideal model delta sigma weight residual 120.24 122.84 -2.60 6.30e-01 2.52e+00 1.70e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 ... (remaining 32795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13664 17.90 - 35.80: 590 35.80 - 53.70: 111 53.70 - 71.61: 17 71.61 - 89.51: 1 Dihedral angle restraints: 14383 sinusoidal: 5491 harmonic: 8892 Sorted by residual: dihedral pdb=" CA LEU B 534 " pdb=" C LEU B 534 " pdb=" N HIS B 535 " pdb=" CA HIS B 535 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA B 401 " pdb=" C ALA B 401 " pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta harmonic sigma weight residual 180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP B 728 " pdb=" CB ASP B 728 " pdb=" CG ASP B 728 " pdb=" OD1 ASP B 728 " ideal model delta sinusoidal sigma weight residual -30.00 -83.13 53.13 1 2.00e+01 2.50e-03 9.60e+00 ... (remaining 14380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3811 0.134 - 0.269: 5 0.269 - 0.403: 4 0.403 - 0.537: 1 0.537 - 0.671: 3 Chirality restraints: 3824 Sorted by residual: chirality pdb=" C62 LLL B1101 " pdb=" C12 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O62 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.49 -3.16 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C42 LLL B1101 " pdb=" C32 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O11 LLL B1101 " both_signs ideal model delta sigma weight residual False 2.54 3.21 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C52 LLL B1101 " pdb=" C42 LLL B1101 " pdb=" C62 LLL B1101 " pdb=" O52 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.47 -3.05 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 3821 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 871 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 872 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 872 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 872 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 830 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 831 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 831 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 831 " -0.017 5.00e-02 4.00e+02 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3475 2.75 - 3.29: 24244 3.29 - 3.82: 40777 3.82 - 4.36: 47709 4.36 - 4.90: 83622 Nonbonded interactions: 199827 Sorted by model distance: nonbonded pdb=" O ALA A 451 " pdb=" OG SER A 878 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 526 " pdb=" O ILE A1016 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR C 526 " pdb=" O ILE C1016 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 153 " pdb=" OH TYR B 182 " model vdw 2.276 2.440 ... (remaining 199822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 505 or ( \ resid 506 and (name N or name CA or name C or name O or name CB )) or (resid 507 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 1031)) selection = (chain 'B' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 499 or ( \ resid 500 through 502 and (name N or name CA or name C or name O or name CB )) o \ r (resid 503 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 or (resid 508 through 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 638 or (resid 639 and (name N or name CA \ or name C or name O or name CB )) or resid 640 through 657 or (resid 658 and (na \ me N or name CA or name C or name O or name CB )) or resid 659 through 1031)) selection = (chain 'C' and (resid 1 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 through 6 \ 57 or (resid 658 and (name N or name CA or name C or name O or name CB )) or res \ id 659 through 1031)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15122 2.51 5 N 3992 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.400 Check model and map are aligned: 0.300 Process input model: 62.370 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.004 0.075 24134 Z= 0.279 Angle : 0.561 10.117 32800 Z= 0.324 Chirality : 0.044 0.671 3824 Planarity : 0.003 0.038 4225 Dihedral : 10.455 89.508 8675 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3091 helix: 2.32 (0.12), residues: 1691 sheet: -0.26 (0.26), residues: 427 loop : 0.04 (0.20), residues: 973 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 640 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 25 residues processed: 696 average time/residue: 0.3717 time to fit residues: 403.1939 Evaluate side-chains 414 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 389 time to evaluate : 2.945 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2234 time to fit residues: 14.3885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 2.9990 chunk 234 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 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 34 GLN A 59 ASN A 81 GLN A 87 GLN A 105 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 213 GLN A 237 GLN A 437 GLN A 439 GLN A 469 GLN A 517 GLN A 583 GLN A 585 GLN A 592 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 213 GLN B 255 GLN B 592 GLN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN B 708 ASN B 724 GLN B 749 GLN B 818 ASN B 926 GLN C 87 GLN C 110 GLN C 120 GLN C 123 GLN C 124 ASN C 241 GLN C 254 ASN C 415 ASN C 576 GLN C 584 GLN C 655 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 700 GLN C 716 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN C 749 GLN C 863 GLN C 967 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 24134 Z= 0.190 Angle : 0.510 8.071 32800 Z= 0.262 Chirality : 0.039 0.139 3824 Planarity : 0.004 0.034 4225 Dihedral : 3.719 38.750 3324 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3091 helix: 2.35 (0.12), residues: 1699 sheet: -0.19 (0.25), residues: 438 loop : 0.14 (0.21), residues: 954 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 423 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 31 residues processed: 465 average time/residue: 0.3491 time to fit residues: 258.9235 Evaluate side-chains 394 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 363 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2283 time to fit residues: 16.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24134 Z= 0.164 Angle : 0.479 9.007 32800 Z= 0.244 Chirality : 0.038 0.193 3824 Planarity : 0.003 0.035 4225 Dihedral : 3.640 32.603 3324 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.93 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1697 sheet: -0.25 (0.25), residues: 441 loop : 0.18 (0.21), residues: 953 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 403 time to evaluate : 2.891 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 22 residues processed: 439 average time/residue: 0.3517 time to fit residues: 247.8280 Evaluate side-chains 378 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 356 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2286 time to fit residues: 13.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.3980 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 0.0470 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 237 GLN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS C 360 GLN C 516 ASN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 24134 Z= 0.250 Angle : 0.503 9.360 32800 Z= 0.257 Chirality : 0.039 0.172 3824 Planarity : 0.003 0.035 4225 Dihedral : 3.683 33.337 3324 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 3091 helix: 2.24 (0.12), residues: 1699 sheet: -0.23 (0.25), residues: 439 loop : 0.13 (0.20), residues: 953 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 361 time to evaluate : 2.664 Fit side-chains outliers start: 70 outliers final: 36 residues processed: 400 average time/residue: 0.3420 time to fit residues: 219.3535 Evaluate side-chains 378 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 342 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2313 time to fit residues: 19.7745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 268 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 152 GLN A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 621 GLN B 870 GLN C 120 GLN C 124 ASN C 360 GLN C 516 ASN C 517 GLN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24134 Z= 0.166 Angle : 0.474 9.277 32800 Z= 0.241 Chirality : 0.038 0.195 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.616 30.998 3324 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.15), residues: 3091 helix: 2.28 (0.13), residues: 1693 sheet: -0.16 (0.24), residues: 443 loop : 0.16 (0.20), residues: 955 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 381 time to evaluate : 2.619 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 405 average time/residue: 0.3626 time to fit residues: 235.1141 Evaluate side-chains 365 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 353 time to evaluate : 3.155 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2559 time to fit residues: 9.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 248 optimal weight: 0.3980 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 120 GLN C 124 ASN C 254 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24134 Z= 0.196 Angle : 0.486 8.612 32800 Z= 0.247 Chirality : 0.038 0.206 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.604 31.400 3324 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.15), residues: 3091 helix: 2.28 (0.13), residues: 1691 sheet: -0.21 (0.24), residues: 455 loop : 0.22 (0.20), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 362 time to evaluate : 2.594 Fit side-chains outliers start: 41 outliers final: 17 residues processed: 387 average time/residue: 0.3563 time to fit residues: 222.2259 Evaluate side-chains 365 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 348 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2338 time to fit residues: 11.3237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 218 optimal weight: 0.0870 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 297 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 231 ASN A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN B 81 GLN C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24134 Z= 0.169 Angle : 0.477 8.586 32800 Z= 0.242 Chirality : 0.038 0.200 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.575 30.374 3324 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.90 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3091 helix: 2.29 (0.13), residues: 1692 sheet: -0.12 (0.24), residues: 453 loop : 0.23 (0.20), residues: 946 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 368 time to evaluate : 3.747 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 385 average time/residue: 0.3530 time to fit residues: 219.0646 Evaluate side-chains 355 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 346 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2254 time to fit residues: 7.5278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 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 319 HIS A 517 GLN A 749 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 136 ASN C 415 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 24134 Z= 0.163 Angle : 0.478 10.075 32800 Z= 0.241 Chirality : 0.038 0.148 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.536 29.951 3324 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.15), residues: 3091 helix: 2.31 (0.13), residues: 1693 sheet: 0.02 (0.25), residues: 435 loop : 0.19 (0.20), residues: 963 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 2.653 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 368 average time/residue: 0.3513 time to fit residues: 208.4893 Evaluate side-chains 349 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 341 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2244 time to fit residues: 6.9965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 4.9990 chunk 285 optimal weight: 0.0470 chunk 260 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 ASN C 254 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 24134 Z= 0.181 Angle : 0.490 10.657 32800 Z= 0.245 Chirality : 0.038 0.254 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.540 29.906 3324 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3091 helix: 2.27 (0.13), residues: 1700 sheet: 0.10 (0.25), residues: 445 loop : 0.18 (0.20), residues: 946 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 344 time to evaluate : 2.888 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 350 average time/residue: 0.3486 time to fit residues: 197.4635 Evaluate side-chains 343 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 339 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2339 time to fit residues: 5.1971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 0.0980 chunk 245 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 ASN C 254 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 24134 Z= 0.177 Angle : 0.491 9.401 32800 Z= 0.245 Chirality : 0.038 0.239 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.536 29.576 3324 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3091 helix: 2.27 (0.13), residues: 1699 sheet: 0.05 (0.24), residues: 459 loop : 0.22 (0.21), residues: 933 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 352 time to evaluate : 3.029 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 355 average time/residue: 0.3535 time to fit residues: 204.2215 Evaluate side-chains 341 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 337 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2291 time to fit residues: 5.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.0270 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 112 GLN C 254 ASN C 517 GLN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091277 restraints weight = 35068.895| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.05 r_work: 0.2977 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 24134 Z= 0.178 Angle : 0.492 9.517 32800 Z= 0.247 Chirality : 0.038 0.226 3824 Planarity : 0.003 0.036 4225 Dihedral : 3.530 29.347 3324 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3091 helix: 2.25 (0.13), residues: 1698 sheet: 0.01 (0.24), residues: 464 loop : 0.21 (0.21), residues: 929 =============================================================================== Job complete usr+sys time: 5513.89 seconds wall clock time: 100 minutes 53.72 seconds (6053.72 seconds total)