Starting phenix.real_space_refine on Fri Mar 15 05:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqe_22997/03_2024/7kqe_22997.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.086 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 S 141 5.16 5 C 22020 2.51 5 N 5793 2.21 5 O 6672 1.98 5 H 33744 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 153": "OE1" <-> "OE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L GLU 207": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 153": "OE1" <-> "OE2" Residue "M TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "I ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 153": "OE1" <-> "OE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68370 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3187 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Chain: "L" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3117 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 16486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 16486 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 16486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 16486 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "C" Number of atoms: 16486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 16486 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "J" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3187 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Chain: "M" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3117 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Chain: "I" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3187 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Chain: "N" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3117 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Time building chain proxies: 22.01, per 1000 atoms: 0.32 Number of scatterers: 68370 At special positions: 0 Unit cell: (186.684, 169.583, 200.934, 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 141 16.00 O 6672 8.00 N 5793 7.00 C 22020 6.00 H 33744 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.01 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.00 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 201 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 91 " distance=2.01 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 197 " distance=2.00 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 145 " - pdb=" SG CYS I 201 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 91 " distance=2.01 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " distance=2.00 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: 41.60 Conformation dependent library (CDL) restraints added in 5.2 seconds 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 90 sheets defined 20.9% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 206 through 209 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.876A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.601A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'A' and resid 70 through 70 No H-bonds generated for 'chain 'A' and resid 70 through 70' Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 147 through 150 removed outlier: 3.503A pdb=" N LYS A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.765A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.485A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.510A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.935A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.602A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.795A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.540A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.013A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.460A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.368A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.510A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.922A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.911A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.568A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 removed outlier: 3.880A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 853 through 856' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.391A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.076A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.801A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 70 No H-bonds generated for 'chain 'C' and resid 70 through 70' Processing helix chain 'C' and resid 76 through 77 No H-bonds generated for 'chain 'C' and resid 76 through 77' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.706A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.316A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.511A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.576A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.560A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.676A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.992A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.357A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.502A pdb=" N LEU C1145 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 206 through 209 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.875A pdb=" N ASN M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 86 removed outlier: 3.601A pdb=" N GLU M 86 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 131 Processing helix chain 'M' and resid 185 through 192 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 206 through 209 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.876A pdb=" N ASN N 32 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 86 removed outlier: 3.601A pdb=" N GLU N 86 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.627A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.848A pdb=" N CYS H 95 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP H 108 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG H 97 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.143A pdb=" N GLY H 144 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 187 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU H 146 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER H 185 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS H 148 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU H 183 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.143A pdb=" N GLY H 144 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 187 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU H 146 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER H 185 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS H 148 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU H 183 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 200 through 205 Processing sheet with id=AA7, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.579A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.579A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 118 through 122 removed outlier: 4.011A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 122 removed outlier: 4.011A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 157 through 158 Processing sheet with id=AB4, first strand: chain 'L' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.965A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.610A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.743A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.842A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.908A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.748A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.451A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.502A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.400A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.881A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.135A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.586A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.131A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.131A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.780A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.074A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.666A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 173 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE B 128 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL B 171 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL B 130 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLU B 169 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.718A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.276A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.613A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.430A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.680A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.882A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.695A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.806A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.177A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.175A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.508A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.021A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.021A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.104A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.765A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.771A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AH1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.636A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AH3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.626A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.848A pdb=" N CYS J 95 " --> pdb=" O TRP J 108 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP J 108 " --> pdb=" O CYS J 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG J 97 " --> pdb=" O ASP J 106 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 125 through 129 removed outlier: 5.142A pdb=" N GLY J 144 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL J 187 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU J 146 " --> pdb=" O SER J 185 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER J 185 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS J 148 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU J 183 " --> pdb=" O LYS J 148 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 125 through 129 removed outlier: 5.142A pdb=" N GLY J 144 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL J 187 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU J 146 " --> pdb=" O SER J 185 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER J 185 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS J 148 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU J 183 " --> pdb=" O LYS J 148 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 200 through 205 Processing sheet with id=AH8, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AH9, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.578A pdb=" N ALA M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.578A pdb=" N ALA M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 118 through 122 removed outlier: 4.011A pdb=" N VAL M 137 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR M 176 " --> pdb=" O ASP M 142 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 118 through 122 removed outlier: 4.011A pdb=" N VAL M 137 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR M 176 " --> pdb=" O ASP M 142 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 157 through 158 Processing sheet with id=AI5, first strand: chain 'M' and resid 157 through 158 Processing sheet with id=AI6, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AI7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.627A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.848A pdb=" N CYS I 95 " --> pdb=" O TRP I 108 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP I 108 " --> pdb=" O CYS I 95 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG I 97 " --> pdb=" O ASP I 106 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 125 through 129 removed outlier: 5.143A pdb=" N GLY I 144 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL I 187 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU I 146 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER I 185 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS I 148 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU I 183 " --> pdb=" O LYS I 148 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 125 through 129 removed outlier: 5.143A pdb=" N GLY I 144 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL I 187 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU I 146 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER I 185 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS I 148 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU I 183 " --> pdb=" O LYS I 148 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 200 through 205 Processing sheet with id=AJ3, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AJ4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.579A pdb=" N ALA N 12 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.579A pdb=" N ALA N 12 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 118 through 122 removed outlier: 4.010A pdb=" N VAL N 137 " --> pdb=" O PHE N 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 118 through 122 removed outlier: 4.010A pdb=" N VAL N 137 " --> pdb=" O PHE N 122 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AJ9, first strand: chain 'N' and resid 157 through 158 1595 hydrogen bonds defined for protein. 4164 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: 29.72 Time building geometry restraints manager: 43.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 33744 1.13 - 1.30: 6024 1.30 - 1.48: 14288 1.48 - 1.65: 14974 1.65 - 1.82: 174 Bond restraints: 69204 Sorted by residual: bond pdb=" N HIS C1088 " pdb=" H HIS C1088 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG C 34 " pdb="HH12 ARG C 34 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE A 565 " pdb=" HE1 PHE A 565 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N THR A 739 " pdb=" H THR A 739 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 PHE C 175 " pdb=" HE2 PHE C 175 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 69199 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.60: 682 104.60 - 112.23: 75408 112.23 - 119.86: 25159 119.86 - 127.48: 23151 127.48 - 135.11: 313 Bond angle restraints: 124713 Sorted by residual: angle pdb=" CA ASN B 125 " pdb=" CB ASN B 125 " pdb=" CG ASN B 125 " ideal model delta sigma weight residual 112.60 120.67 -8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" CA ASP A 80 " pdb=" CB ASP A 80 " pdb=" CG ASP A 80 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.86e+01 angle pdb=" O HIS A1083 " pdb=" C HIS A1083 " pdb=" N ASP A1084 " ideal model delta sigma weight residual 122.59 114.80 7.79 1.33e+00 5.65e-01 3.43e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.77 -7.07 1.22e+00 6.72e-01 3.36e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.69 -6.99 1.22e+00 6.72e-01 3.28e+01 ... (remaining 124708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 29780 17.97 - 35.93: 1935 35.93 - 53.90: 799 53.90 - 71.87: 763 71.87 - 89.84: 47 Dihedral angle restraints: 33324 sinusoidal: 17823 harmonic: 15501 Sorted by residual: dihedral pdb=" CA LEU A 441 " pdb=" C LEU A 441 " pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA J 141 " pdb=" C ALA J 141 " pdb=" N ALA J 142 " pdb=" CA ALA J 142 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA H 141 " pdb=" C ALA H 141 " pdb=" N ALA H 142 " pdb=" CA ALA H 142 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 33321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3842 0.099 - 0.198: 1400 0.198 - 0.296: 172 0.296 - 0.395: 40 0.395 - 0.494: 6 Chirality restraints: 5460 Sorted by residual: chirality pdb=" CA ARG C1107 " pdb=" N ARG C1107 " pdb=" C ARG C1107 " pdb=" CB ARG C1107 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ASN B 370 " pdb=" N ASN B 370 " pdb=" C ASN B 370 " pdb=" CB ASN B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 5457 not shown) Planarity restraints: 10440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 258 " 0.210 2.00e-02 2.50e+03 9.45e-02 3.57e+02 pdb=" CG TRP A 258 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 258 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 258 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP A 258 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP A 258 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 258 " -0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 258 " 0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 258 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 258 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP A 258 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP A 258 " -0.165 2.00e-02 2.50e+03 pdb=" HE3 TRP A 258 " -0.167 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 258 " 0.050 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 258 " -0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP A 258 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " -0.131 2.00e-02 2.50e+03 7.81e-02 2.44e+02 pdb=" CG TRP C 64 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " 0.052 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " 0.096 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 TRP C 64 " -0.060 2.00e-02 2.50e+03 pdb=" HE1 TRP C 64 " 0.072 2.00e-02 2.50e+03 pdb=" HE3 TRP C 64 " 0.133 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 64 " 0.023 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 64 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP C 64 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 79 " -0.221 2.00e-02 2.50e+03 8.62e-02 2.23e+02 pdb=" CG PHE A 79 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 79 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 79 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 79 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 79 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 79 " -0.038 2.00e-02 2.50e+03 pdb=" HD1 PHE A 79 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 PHE A 79 " 0.080 2.00e-02 2.50e+03 pdb=" HE1 PHE A 79 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 79 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 79 " -0.109 2.00e-02 2.50e+03 ... (remaining 10437 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 4558 2.17 - 2.78: 120253 2.78 - 3.39: 191469 3.39 - 3.99: 262084 3.99 - 4.60: 381373 Nonbonded interactions: 959737 Sorted by model distance: nonbonded pdb=" HG SER B 555 " pdb=" OD1 ASP B 586 " model vdw 1.566 1.850 nonbonded pdb=" HG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 1.573 1.850 nonbonded pdb=" OE2 GLU A 918 " pdb=" HG SER C1123 " model vdw 1.576 1.850 nonbonded pdb=" H SER M 118 " pdb=" HG SER M 118 " model vdw 1.577 2.100 nonbonded pdb=" H SER L 118 " pdb=" HG SER L 118 " model vdw 1.577 2.100 ... (remaining 959732 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 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: 1.050 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: 0.780 Extract box with map and model: 8.160 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 165.790 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.260 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3763 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 : 0.012 0.047 35460 Z= 0.787 Angle : 1.796 8.073 48312 Z= 1.209 Chirality : 0.098 0.494 5460 Planarity : 0.014 0.200 6246 Dihedral : 13.986 89.467 12639 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 1.08 % Allowed : 4.89 % Favored : 94.02 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.66 % 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: -1.09 (0.12), residues: 4413 helix: -0.57 (0.17), residues: 692 sheet: 0.26 (0.15), residues: 1086 loop : -1.23 (0.11), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.023 TRP A 258 HIS 0.016 0.003 HIS A 207 PHE 0.121 0.014 PHE A 79 TYR 0.122 0.020 TYR B 660 ARG 0.011 0.002 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 4.128 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: 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: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.7864 (tpt-90) cc_final: 0.7603 (ttm110) REVERT: B 544 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8584 (m-40) REVERT: C 1072 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: C 1092 GLU cc_start: 0.8598 (tt0) cc_final: 0.8332 (pm20) outliers start: 42 outliers final: 15 residues processed: 149 average time/residue: 2.5798 time to fit residues: 467.4786 Evaluate side-chains 85 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 175 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 336 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 61 ASN A 164 ASN A 354 ASN A 437 ASN A 487 ASN A 703 ASN A 787 GLN A 919 ASN A 925 ASN A1064 HIS A1088 HIS B 125 ASN B 354 ASN B 437 ASN B 616 ASN B 703 ASN B 925 ASN B1064 HIS B1083 HIS C 52 GLN C 354 ASN C 437 ASN C 992 GLN C1023 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3697 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35460 Z= 0.236 Angle : 0.658 7.759 48312 Z= 0.362 Chirality : 0.045 0.181 5460 Planarity : 0.005 0.053 6246 Dihedral : 7.478 75.153 4815 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 1.34 % Allowed : 6.34 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.87 (0.12), residues: 4413 helix: 0.72 (0.19), residues: 708 sheet: -0.10 (0.15), residues: 1184 loop : -1.22 (0.11), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.006 0.001 HIS N 192 PHE 0.020 0.001 PHE A 79 TYR 0.024 0.002 TYR C 369 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 78 time to evaluate : 4.160 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: 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: symmetry clash revert: symmetry clash REVERT: A 786 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8459 (pmtt) REVERT: A 1019 ARG cc_start: 0.7745 (tpt-90) cc_final: 0.7539 (ttm110) REVERT: B 544 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: B 988 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8748 (mp0) outliers start: 52 outliers final: 18 residues processed: 119 average time/residue: 2.8015 time to fit residues: 401.1745 Evaluate side-chains 89 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 175 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 436 optimal weight: 50.0000 chunk 359 optimal weight: 0.4980 chunk 400 optimal weight: 50.0000 chunk 137 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 703 ASN C 439 ASN C 607 GLN C1064 HIS C1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3723 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35460 Z= 0.207 Angle : 0.548 6.352 48312 Z= 0.296 Chirality : 0.043 0.164 5460 Planarity : 0.004 0.047 6246 Dihedral : 6.033 57.221 4802 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.03 % Allowed : 7.47 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4413 helix: 1.55 (0.20), residues: 701 sheet: -0.20 (0.14), residues: 1240 loop : -0.93 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 100 HIS 0.006 0.001 HIS A1088 PHE 0.034 0.001 PHE N 2 TYR 0.020 0.001 TYR C 369 ARG 0.012 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 75 time to evaluate : 4.166 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: 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 456 PHE cc_start: 0.9247 (m-80) cc_final: 0.9040 (m-80) REVERT: A 786 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8518 (pmtt) REVERT: A 1019 ARG cc_start: 0.7887 (tpt-90) cc_final: 0.7649 (ttm110) REVERT: B 544 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8504 (m-40) REVERT: B 697 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6243 (ptp) REVERT: C 615 VAL cc_start: 0.6557 (t) cc_final: 0.6226 (m) REVERT: C 869 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6933 (mtm) outliers start: 40 outliers final: 11 residues processed: 109 average time/residue: 2.5903 time to fit residues: 345.2897 Evaluate side-chains 80 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 40.0000 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 429 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 384 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 703 ASN A1083 HIS B 52 GLN B1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3753 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35460 Z= 0.304 Angle : 0.541 6.776 48312 Z= 0.293 Chirality : 0.043 0.184 5460 Planarity : 0.004 0.075 6246 Dihedral : 5.621 42.153 4788 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.90 % Allowed : 8.27 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4413 helix: 1.68 (0.20), residues: 692 sheet: -0.24 (0.14), residues: 1248 loop : -0.90 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 100 HIS 0.004 0.001 HIS B1088 PHE 0.013 0.001 PHE I 78 TYR 0.017 0.001 TYR C 369 ARG 0.006 0.000 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 68 time to evaluate : 4.128 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: 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 786 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8452 (pmtt) REVERT: A 1019 ARG cc_start: 0.7871 (tpt-90) cc_final: 0.7618 (ttm110) REVERT: B 544 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: C 440 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8405 (p0) outliers start: 35 outliers final: 16 residues processed: 99 average time/residue: 2.6516 time to fit residues: 321.3171 Evaluate side-chains 79 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 385 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3756 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35460 Z= 0.245 Angle : 0.517 6.209 48312 Z= 0.276 Chirality : 0.043 0.158 5460 Planarity : 0.004 0.048 6246 Dihedral : 5.290 39.339 4788 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.90 % Allowed : 8.84 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 4413 helix: 1.91 (0.20), residues: 689 sheet: -0.26 (0.14), residues: 1259 loop : -0.83 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 100 HIS 0.004 0.001 HIS A1083 PHE 0.019 0.001 PHE C 342 TYR 0.017 0.001 TYR C 369 ARG 0.009 0.001 ARG N 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 62 time to evaluate : 4.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 786 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8447 (pmtt) REVERT: B 544 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: B 697 MET cc_start: 0.7349 (ptm) cc_final: 0.7121 (ptp) REVERT: C 440 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8666 (p0) outliers start: 35 outliers final: 15 residues processed: 92 average time/residue: 2.6312 time to fit residues: 298.5521 Evaluate side-chains 70 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 251 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 429 optimal weight: 40.0000 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3750 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35460 Z= 0.168 Angle : 0.488 7.312 48312 Z= 0.258 Chirality : 0.043 0.160 5460 Planarity : 0.004 0.053 6246 Dihedral : 4.947 31.477 4786 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.70 % Allowed : 9.20 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4413 helix: 2.32 (0.21), residues: 681 sheet: -0.21 (0.14), residues: 1261 loop : -0.69 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 100 HIS 0.003 0.001 HIS A1088 PHE 0.031 0.001 PHE J 151 TYR 0.015 0.001 TYR C 369 ARG 0.006 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 4.176 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 544 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8589 (m-40) REVERT: B 697 MET cc_start: 0.7303 (ptm) cc_final: 0.7053 (ptp) REVERT: C 615 VAL cc_start: 0.6204 (t) cc_final: 0.5837 (m) outliers start: 27 outliers final: 18 residues processed: 78 average time/residue: 2.5227 time to fit residues: 244.6719 Evaluate side-chains 72 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 361 optimal weight: 30.0000 chunk 239 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A1023 ASN A1135 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3777 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35460 Z= 0.336 Angle : 0.520 5.831 48312 Z= 0.277 Chirality : 0.043 0.155 5460 Planarity : 0.004 0.051 6246 Dihedral : 4.961 30.681 4786 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.88 % Allowed : 9.35 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4413 helix: 2.07 (0.20), residues: 690 sheet: -0.28 (0.14), residues: 1269 loop : -0.73 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.004 0.001 HIS B1064 PHE 0.011 0.001 PHE C 342 TYR 0.015 0.001 TYR A 369 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 52 time to evaluate : 4.171 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: L 3 MET cc_start: 0.3349 (tpp) cc_final: 0.3086 (tpp) REVERT: B 544 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8519 (m-40) REVERT: B 697 MET cc_start: 0.7287 (ptm) cc_final: 0.7059 (ptp) REVERT: C 440 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8829 (p0) outliers start: 34 outliers final: 19 residues processed: 84 average time/residue: 2.2827 time to fit residues: 243.0444 Evaluate side-chains 71 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 336 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 201 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3776 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35460 Z= 0.271 Angle : 0.504 5.640 48312 Z= 0.268 Chirality : 0.043 0.154 5460 Planarity : 0.004 0.052 6246 Dihedral : 4.864 30.786 4786 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.80 % Allowed : 9.56 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4413 helix: 2.11 (0.20), residues: 688 sheet: -0.29 (0.13), residues: 1284 loop : -0.71 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS C1048 PHE 0.020 0.001 PHE J 151 TYR 0.016 0.001 TYR B1067 ARG 0.007 0.000 ARG I 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 53 time to evaluate : 4.297 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 MET cc_start: 0.3399 (tpp) cc_final: 0.3155 (tpp) REVERT: B 544 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8511 (m-40) REVERT: B 697 MET cc_start: 0.7273 (ptm) cc_final: 0.7041 (ptp) REVERT: C 615 VAL cc_start: 0.6279 (t) cc_final: 0.5899 (m) outliers start: 31 outliers final: 21 residues processed: 80 average time/residue: 2.4741 time to fit residues: 248.0373 Evaluate side-chains 73 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 40.0000 chunk 409 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 398 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 313 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 360 optimal weight: 30.0000 chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3788 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35460 Z= 0.331 Angle : 0.523 6.790 48312 Z= 0.278 Chirality : 0.043 0.152 5460 Planarity : 0.004 0.052 6246 Dihedral : 4.862 30.356 4786 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.77 % Allowed : 9.71 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4413 helix: 2.01 (0.20), residues: 687 sheet: -0.34 (0.14), residues: 1283 loop : -0.73 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.006 0.001 HIS A 207 PHE 0.017 0.001 PHE A 175 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG M 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 52 time to evaluate : 4.220 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 MET cc_start: 0.3137 (tpp) cc_final: 0.2907 (tpp) REVERT: B 544 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8407 (m-40) REVERT: B 697 MET cc_start: 0.7267 (ptm) cc_final: 0.7023 (ptp) REVERT: C 440 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8829 (p0) outliers start: 30 outliers final: 21 residues processed: 77 average time/residue: 2.2911 time to fit residues: 222.5538 Evaluate side-chains 74 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 51 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 62 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 6.9990 chunk 421 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 293 optimal weight: 30.0000 chunk 442 optimal weight: 40.0000 chunk 407 optimal weight: 10.0000 chunk 352 optimal weight: 0.6980 chunk 36 optimal weight: 40.0000 chunk 272 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3782 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35460 Z= 0.254 Angle : 0.499 5.514 48312 Z= 0.264 Chirality : 0.043 0.150 5460 Planarity : 0.004 0.052 6246 Dihedral : 4.759 30.427 4786 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.57 % Allowed : 9.92 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4413 helix: 2.15 (0.20), residues: 687 sheet: -0.27 (0.14), residues: 1289 loop : -0.67 (0.13), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS L 201 PHE 0.015 0.001 PHE J 151 TYR 0.020 0.001 TYR B 449 ARG 0.005 0.000 ARG M 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 4.329 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 MET cc_start: 0.3163 (tpp) cc_final: 0.2956 (tpp) REVERT: B 544 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8412 (m-40) REVERT: B 697 MET cc_start: 0.7266 (ptm) cc_final: 0.7019 (ptp) REVERT: C 440 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8829 (p0) outliers start: 22 outliers final: 18 residues processed: 75 average time/residue: 2.4814 time to fit residues: 234.6871 Evaluate side-chains 73 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 CYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 4.9990 chunk 375 optimal weight: 50.0000 chunk 107 optimal weight: 0.6980 chunk 324 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 362 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 856 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.086698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.054556 restraints weight = 570110.464| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.85 r_work: 0.2946 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35460 Z= 0.149 Angle : 0.475 6.316 48312 Z= 0.248 Chirality : 0.042 0.154 5460 Planarity : 0.004 0.051 6246 Dihedral : 4.590 30.162 4786 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.62 % Allowed : 10.05 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4413 helix: 2.46 (0.21), residues: 681 sheet: -0.19 (0.14), residues: 1288 loop : -0.57 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.004 0.001 HIS L 201 PHE 0.015 0.001 PHE J 151 TYR 0.015 0.001 TYR B 369 ARG 0.004 0.000 ARG M 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11602.95 seconds wall clock time: 203 minutes 7.24 seconds (12187.24 seconds total)