Starting phenix.real_space_refine on Mon Jul 22 06:52:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/07_2024/8u1s_41826.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 11044 2.51 5 N 2966 2.21 5 O 3323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17465 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2613 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain breaks: 4 Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "K" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 315} Chain breaks: 4 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2548 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 4 Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2569 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 316} Chain breaks: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.16, per 1000 atoms: 0.58 Number of scatterers: 17465 At special positions: 0 Unit cell: (168.2, 168.2, 70.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3323 8.00 N 2966 7.00 C 11044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.01 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=1.83 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.01 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.01 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.05 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.01 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.12 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 284 " " NAG B 501 " - " ASN B 284 " " NAG C 501 " - " ASN C 284 " " NAG D 501 " - " ASN D 284 " Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 3.2 seconds 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 45 sheets defined 2.7% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 67 removed outlier: 5.849A pdb=" N SER G 65 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.990A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) 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 97 through 100B Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.077A pdb=" N ASP B 390 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.768A pdb=" N ILE A 445 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 97 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 443 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 removed outlier: 5.623A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 174 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER A 158 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A 172 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.529A pdb=" N SER A 178 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A 212 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 206 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.624A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.554A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 286 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 281 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 288 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS A 279 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA A 290 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYS A 277 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 8.106A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.000A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.454A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 12 removed outlier: 5.957A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.559A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 8.268A pdb=" N TYR E 34 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER E 52 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.596A pdb=" N ALA F 84 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 8.416A pdb=" N TYR H 34 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.764A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.585A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 93 through 98 removed outlier: 6.803A pdb=" N ILE B 445 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 97 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 443 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 123 removed outlier: 5.502A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 174 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 158 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE B 172 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.511A pdb=" N SER B 178 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 206 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AD2, first strand: chain 'B' and resid 223 through 224 removed outlier: 6.508A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 268 through 269 removed outlier: 7.390A pdb=" N THR B 286 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 281 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 288 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS B 279 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA B 290 " --> pdb=" O CYS B 277 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS B 277 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 352 through 356 removed outlier: 7.002A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 93 through 98 removed outlier: 6.853A pdb=" N ILE C 445 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU C 97 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 443 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 123 removed outlier: 5.566A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 126 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.898A pdb=" N SER C 178 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD9, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.644A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.694A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR C 286 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE C 281 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU C 288 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 290 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS C 277 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 removed outlier: 7.027A pdb=" N MET C 375 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 377 " --> pdb=" O MET C 400 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 381 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 396 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.839A pdb=" N ILE D 445 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU D 97 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR D 443 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 115 through 123 removed outlier: 5.449A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS D 155 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER D 158 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE D 172 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS D 160 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N SER D 170 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 179 through 183 removed outlier: 6.167A pdb=" N TYR D 206 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.941A pdb=" N GLU D 250 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.622A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR D 286 " --> pdb=" O PHE D 281 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE D 281 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU D 288 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS D 279 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA D 290 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N CYS D 277 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 352 through 354 removed outlier: 7.318A pdb=" N MET D 375 " --> pdb=" O PRO D 402 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET D 377 " --> pdb=" O MET D 400 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 381 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE D 396 " --> pdb=" O VAL D 381 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1527 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: 6.10 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3876 1.32 - 1.46: 6319 1.46 - 1.60: 7488 1.60 - 1.75: 59 1.75 - 1.89: 147 Bond restraints: 17889 Sorted by residual: bond pdb=" CB HIS D 354 " pdb=" CG HIS D 354 " ideal model delta sigma weight residual 1.497 1.369 0.128 1.40e-02 5.10e+03 8.42e+01 bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.24e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.11e+01 bond pdb=" CB HIS B 354 " pdb=" CG HIS B 354 " ideal model delta sigma weight residual 1.497 1.377 0.120 1.40e-02 5.10e+03 7.40e+01 bond pdb=" CB LEU C 454 " pdb=" CG LEU C 454 " ideal model delta sigma weight residual 1.530 1.676 -0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 17884 not shown) Histogram of bond angle deviations from ideal: 93.69 - 101.85: 85 101.85 - 110.01: 4486 110.01 - 118.18: 9266 118.18 - 126.34: 10033 126.34 - 134.50: 337 Bond angle restraints: 24207 Sorted by residual: angle pdb=" C PRO F 59 " pdb=" N SER F 60 " pdb=" CA SER F 60 " ideal model delta sigma weight residual 122.31 99.32 22.99 2.00e+00 2.50e-01 1.32e+02 angle pdb=" N TYR F 94 " pdb=" CA TYR F 94 " pdb=" CB TYR F 94 " ideal model delta sigma weight residual 110.25 125.19 -14.94 1.36e+00 5.41e-01 1.21e+02 angle pdb=" N SER K 95 " pdb=" CA SER K 95 " pdb=" C SER K 95 " ideal model delta sigma weight residual 114.56 101.67 12.89 1.27e+00 6.20e-01 1.03e+02 angle pdb=" C GLY B 335 " pdb=" N PRO B 336 " pdb=" CA PRO B 336 " ideal model delta sigma weight residual 120.21 128.12 -7.91 9.60e-01 1.09e+00 6.78e+01 angle pdb=" N LYS A 371 " pdb=" CA LYS A 371 " pdb=" C LYS A 371 " ideal model delta sigma weight residual 113.28 103.28 10.00 1.22e+00 6.72e-01 6.72e+01 ... (remaining 24202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10297 17.92 - 35.84: 313 35.84 - 53.76: 67 53.76 - 71.67: 33 71.67 - 89.59: 13 Dihedral angle restraints: 10723 sinusoidal: 4336 harmonic: 6387 Sorted by residual: dihedral pdb=" CD ARG G 95 " pdb=" NE ARG G 95 " pdb=" CZ ARG G 95 " pdb=" NH1 ARG G 95 " ideal model delta sinusoidal sigma weight residual 0.00 81.07 -81.07 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 229 " pdb=" CB CYS D 229 " ideal model delta sinusoidal sigma weight residual 93.00 39.55 53.45 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" N TYR F 94 " pdb=" C TYR F 94 " pdb=" CA TYR F 94 " pdb=" CB TYR F 94 " ideal model delta harmonic sigma weight residual 122.80 137.00 -14.20 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 10720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1968 0.112 - 0.224: 559 0.224 - 0.335: 67 0.335 - 0.447: 15 0.447 - 0.559: 6 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 284 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CG LEU C 454 " pdb=" CB LEU C 454 " pdb=" CD1 LEU C 454 " pdb=" CD2 LEU C 454 " both_signs ideal model delta sigma weight residual False -2.59 -3.11 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CB ILE D 114 " pdb=" CA ILE D 114 " pdb=" CG1 ILE D 114 " pdb=" CG2 ILE D 114 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 2612 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.174 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" C7 NAG B 501 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 95 " -1.108 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG G 95 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 95 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG G 95 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 95 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 330 " 0.029 2.00e-02 2.50e+03 6.05e-02 3.65e+01 pdb=" C ASP D 330 " -0.104 2.00e-02 2.50e+03 pdb=" O ASP D 330 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY D 331 " 0.034 2.00e-02 2.50e+03 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 3248 2.75 - 3.47: 22362 3.47 - 4.18: 46584 4.18 - 4.90: 78074 Nonbonded interactions: 150272 Sorted by model distance: nonbonded pdb=" OH TYR A 214 " pdb=" NH2 ARG A 252 " model vdw 1.314 2.520 nonbonded pdb=" NE ARG A 252 " pdb=" OE2 GLU A 264 " model vdw 1.548 2.520 nonbonded pdb=" CE2 TYR I 94 " pdb=" OE1 GLU C 338 " model vdw 1.749 3.340 nonbonded pdb=" OE1 GLU A 338 " pdb=" CE1 TYR L 94 " model vdw 1.955 3.340 nonbonded pdb=" OD1 ASP J 101 " pdb=" CD2 TYR J 102 " model vdw 2.081 3.340 ... (remaining 150267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 78 through 100 or resid 115 through 150 or resid 155 throu \ gh 441 or resid 443 through 454 or resid 501)) selection = (chain 'B' and (resid 78 through 430 or resid 441 or resid 443 through 454 or re \ sid 501)) selection = chain 'C' selection = (chain 'D' and (resid 78 through 100 or resid 115 through 441 or resid 443 throu \ gh 454 or resid 501)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 2.200 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: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 47.730 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.023 0.159 17889 Z= 1.501 Angle : 1.948 22.986 24207 Z= 1.282 Chirality : 0.105 0.559 2615 Planarity : 0.014 0.496 3063 Dihedral : 10.173 89.593 6537 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.04 % Favored : 93.32 % Rotamer: Outliers : 0.79 % Allowed : 1.16 % Favored : 98.05 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 7.41 % 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: -0.28 (0.17), residues: 2185 helix: -4.85 (0.33), residues: 6 sheet: 0.59 (0.18), residues: 831 loop : -0.66 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.012 TRP E 103 HIS 0.016 0.003 HIS B 273 PHE 0.053 0.007 PHE J 78 TYR 0.079 0.009 TYR A 322 ARG 0.012 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 678 time to evaluate : 2.321 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: A 134 HIS cc_start: 0.7413 (t70) cc_final: 0.7087 (t-170) REVERT: A 241 THR cc_start: 0.8068 (t) cc_final: 0.7700 (m) REVERT: J 32 THR cc_start: 0.7756 (p) cc_final: 0.7310 (t) REVERT: G 102 TYR cc_start: 0.7612 (m-80) cc_final: 0.7392 (m-10) REVERT: I 35 TRP cc_start: 0.6981 (m100) cc_final: 0.6680 (m100) REVERT: F 18 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7642 (ttm170) REVERT: C 116 ARG cc_start: 0.7166 (mmm-85) cc_final: 0.6911 (mmm160) REVERT: C 117 GLU cc_start: 0.7760 (mp0) cc_final: 0.7379 (mp0) REVERT: D 338 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6478 (tp30) outliers start: 15 outliers final: 7 residues processed: 689 average time/residue: 0.3351 time to fit residues: 332.8777 Evaluate side-chains 421 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 413 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 338 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 235 ASN J 3 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN F 79 GLN F 89 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 329 ASN C 220 ASN C 230 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 17889 Z= 0.315 Angle : 0.824 11.112 24207 Z= 0.445 Chirality : 0.051 0.272 2615 Planarity : 0.005 0.043 3063 Dihedral : 7.009 58.083 2529 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.03 % Favored : 94.37 % Rotamer: Outliers : 4.43 % Allowed : 11.17 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.31 (0.16), residues: 907 loop : -1.13 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 408 HIS 0.009 0.002 HIS D 173 PHE 0.029 0.003 PHE E 100E TYR 0.028 0.002 TYR K 91 ARG 0.008 0.001 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 494 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.7518 (t70) cc_final: 0.7094 (t-170) REVERT: A 151 ASN cc_start: 0.6123 (t0) cc_final: 0.5052 (m-40) REVERT: A 232 ILE cc_start: 0.8689 (mt) cc_final: 0.8466 (tp) REVERT: J 32 THR cc_start: 0.7902 (p) cc_final: 0.7439 (t) REVERT: K 5 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (p) REVERT: K 18 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8161 (ttm170) REVERT: I 27 GLN cc_start: 0.8343 (mt0) cc_final: 0.8046 (mt0) REVERT: B 295 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7417 (tpp-160) REVERT: B 405 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7204 (mp0) REVERT: C 116 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6868 (mmm160) REVERT: C 117 GLU cc_start: 0.7734 (mp0) cc_final: 0.7160 (mp0) REVERT: C 403 MET cc_start: 0.8111 (ppp) cc_final: 0.7907 (ppp) REVERT: D 215 HIS cc_start: 0.7182 (m-70) cc_final: 0.6752 (m90) REVERT: D 333 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5095 (pt) outliers start: 84 outliers final: 52 residues processed: 540 average time/residue: 0.3144 time to fit residues: 255.1663 Evaluate side-chains 469 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 415 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 165 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 159 optimal weight: 9.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN G 3 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN E 3 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN B 220 ASN C 169 ASN D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17889 Z= 0.212 Angle : 0.707 7.126 24207 Z= 0.378 Chirality : 0.047 0.231 2615 Planarity : 0.005 0.049 3063 Dihedral : 6.107 57.200 2522 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.45 % Favored : 94.10 % Rotamer: Outliers : 3.85 % Allowed : 14.01 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.39 (0.16), residues: 899 loop : -1.22 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 388 HIS 0.007 0.002 HIS A 354 PHE 0.021 0.002 PHE E 100E TYR 0.022 0.002 TYR L 94 ARG 0.018 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 451 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 134 HIS cc_start: 0.7442 (t70) cc_final: 0.6977 (t-170) REVERT: A 232 ILE cc_start: 0.8692 (mt) cc_final: 0.8456 (tp) REVERT: J 32 THR cc_start: 0.7906 (p) cc_final: 0.7389 (t) REVERT: K 5 THR cc_start: 0.8404 (m) cc_final: 0.8198 (p) REVERT: I 27 GLN cc_start: 0.8396 (mt0) cc_final: 0.8116 (mt0) REVERT: I 49 TYR cc_start: 0.6649 (m-10) cc_final: 0.6446 (m-10) REVERT: B 295 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.7414 (tpp-160) REVERT: B 403 MET cc_start: 0.7612 (mtp) cc_final: 0.7354 (ttm) REVERT: B 405 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7191 (mp0) REVERT: C 117 GLU cc_start: 0.7702 (mp0) cc_final: 0.7148 (mp0) REVERT: D 215 HIS cc_start: 0.7007 (m-70) cc_final: 0.6721 (m90) REVERT: D 333 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.5105 (pt) outliers start: 73 outliers final: 53 residues processed: 488 average time/residue: 0.2924 time to fit residues: 213.7606 Evaluate side-chains 445 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 391 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 53 ASN K 79 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN E 3 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN D 220 ASN D 230 ASN D 235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17889 Z= 0.306 Angle : 0.709 8.332 24207 Z= 0.379 Chirality : 0.047 0.222 2615 Planarity : 0.005 0.052 3063 Dihedral : 5.879 59.256 2522 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.13 % Favored : 93.46 % Rotamer: Outliers : 4.85 % Allowed : 15.02 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.92 (0.18), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.19 (0.17), residues: 918 loop : -1.24 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 177 HIS 0.007 0.002 HIS D 173 PHE 0.023 0.002 PHE E 100E TYR 0.021 0.002 TYR L 94 ARG 0.008 0.001 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 416 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 134 HIS cc_start: 0.7382 (t70) cc_final: 0.6878 (t-170) REVERT: G 34 TYR cc_start: 0.8345 (m-80) cc_final: 0.8135 (m-80) REVERT: I 27 GLN cc_start: 0.8393 (mt0) cc_final: 0.8104 (mt0) REVERT: I 49 TYR cc_start: 0.6795 (m-10) cc_final: 0.6541 (m-10) REVERT: B 402 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8256 (Cg_endo) REVERT: B 403 MET cc_start: 0.7604 (mtp) cc_final: 0.7402 (ttm) REVERT: C 117 GLU cc_start: 0.7763 (mp0) cc_final: 0.7177 (mp0) REVERT: D 215 HIS cc_start: 0.7145 (m-70) cc_final: 0.6813 (m90) outliers start: 92 outliers final: 63 residues processed: 463 average time/residue: 0.2929 time to fit residues: 203.4181 Evaluate side-chains 455 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 392 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17889 Z= 0.402 Angle : 0.765 9.436 24207 Z= 0.405 Chirality : 0.049 0.219 2615 Planarity : 0.005 0.047 3063 Dihedral : 5.872 57.638 2519 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.23 % Favored : 92.40 % Rotamer: Outliers : 5.95 % Allowed : 14.96 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.32 (0.17), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.11 (0.17), residues: 908 loop : -1.47 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 32 HIS 0.007 0.002 HIS D 129 PHE 0.023 0.002 PHE E 100E TYR 0.027 0.002 TYR L 94 ARG 0.008 0.001 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 410 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 134 HIS cc_start: 0.7329 (t70) cc_final: 0.6840 (t-170) REVERT: E 5 GLN cc_start: 0.8316 (mp-120) cc_final: 0.7788 (mp10) REVERT: E 82 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7920 (mp) REVERT: E 100 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.3955 (t80) REVERT: B 295 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7380 (tpp80) REVERT: B 403 MET cc_start: 0.7748 (mtp) cc_final: 0.7529 (ttm) REVERT: C 117 GLU cc_start: 0.7776 (mp0) cc_final: 0.7285 (mp0) REVERT: C 169 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7177 (t0) REVERT: C 449 MET cc_start: 0.7326 (ptp) cc_final: 0.6939 (ptp) REVERT: D 215 HIS cc_start: 0.7269 (m-70) cc_final: 0.6898 (m90) outliers start: 113 outliers final: 84 residues processed: 473 average time/residue: 0.2958 time to fit residues: 207.2790 Evaluate side-chains 471 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 384 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 352 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN E 3 GLN C 134 HIS C 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17889 Z= 0.214 Angle : 0.683 9.425 24207 Z= 0.359 Chirality : 0.047 0.480 2615 Planarity : 0.005 0.058 3063 Dihedral : 5.522 56.889 2519 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.18 % Favored : 93.50 % Rotamer: Outliers : 4.85 % Allowed : 17.18 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.25 (0.18), residues: 2185 helix: -4.86 (0.34), residues: 6 sheet: -0.09 (0.17), residues: 905 loop : -1.41 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.006 0.001 HIS D 173 PHE 0.017 0.002 PHE C 413 TYR 0.024 0.001 TYR L 94 ARG 0.014 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 423 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.7102 (t70) cc_final: 0.6662 (t-170) REVERT: I 49 TYR cc_start: 0.6746 (m-10) cc_final: 0.6510 (m-10) REVERT: E 82 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7919 (mp) REVERT: E 100 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (t80) REVERT: E 100 PHE cc_start: 0.4544 (OUTLIER) cc_final: 0.3789 (t80) REVERT: B 134 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7266 (m90) REVERT: B 295 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7369 (tpp80) REVERT: C 424 CYS cc_start: 0.5716 (m) cc_final: 0.5480 (m) REVERT: D 215 HIS cc_start: 0.7122 (m-70) cc_final: 0.6792 (m90) outliers start: 92 outliers final: 66 residues processed: 472 average time/residue: 0.3218 time to fit residues: 229.0850 Evaluate side-chains 453 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 383 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 chunk 97 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN E 3 GLN H 105 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN D 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17889 Z= 0.207 Angle : 0.674 9.206 24207 Z= 0.354 Chirality : 0.047 0.419 2615 Planarity : 0.005 0.090 3063 Dihedral : 5.360 56.722 2519 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.41 % Favored : 93.27 % Rotamer: Outliers : 4.11 % Allowed : 18.76 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.27 (0.18), residues: 2185 helix: -4.86 (0.34), residues: 6 sheet: -0.12 (0.17), residues: 930 loop : -1.43 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 35 HIS 0.008 0.001 HIS D 173 PHE 0.015 0.001 PHE E 100E TYR 0.029 0.001 TYR L 94 ARG 0.010 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 407 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.7017 (t70) cc_final: 0.6605 (t-170) REVERT: I 49 TYR cc_start: 0.6622 (m-10) cc_final: 0.6417 (m-10) REVERT: E 100 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8153 (t80) REVERT: E 100 PHE cc_start: 0.4383 (OUTLIER) cc_final: 0.3543 (t80) REVERT: B 134 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.7233 (m90) REVERT: C 134 HIS cc_start: 0.6474 (t70) cc_final: 0.5350 (p-80) REVERT: D 215 HIS cc_start: 0.7081 (m-70) cc_final: 0.6820 (m90) outliers start: 78 outliers final: 64 residues processed: 449 average time/residue: 0.2928 time to fit residues: 197.2896 Evaluate side-chains 456 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 389 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.0270 chunk 63 optimal weight: 0.0170 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 104 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN E 3 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17889 Z= 0.232 Angle : 0.683 10.670 24207 Z= 0.357 Chirality : 0.046 0.398 2615 Planarity : 0.005 0.056 3063 Dihedral : 5.333 55.885 2518 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.82 % Favored : 92.86 % Rotamer: Outliers : 4.43 % Allowed : 19.39 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.30 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.14 (0.17), residues: 921 loop : -1.44 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 35A HIS 0.007 0.001 HIS D 173 PHE 0.015 0.002 PHE A 413 TYR 0.028 0.001 TYR C 206 ARG 0.011 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 400 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.5105 (t) cc_final: 0.4882 (t) REVERT: A 134 HIS cc_start: 0.6992 (t70) cc_final: 0.6557 (t-170) REVERT: J 100 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.4807 (t80) REVERT: I 49 TYR cc_start: 0.6631 (m-10) cc_final: 0.6423 (m-10) REVERT: E 100 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (t80) REVERT: E 100 PHE cc_start: 0.4294 (OUTLIER) cc_final: 0.3457 (t80) REVERT: D 215 HIS cc_start: 0.7021 (m-70) cc_final: 0.6734 (m90) outliers start: 84 outliers final: 65 residues processed: 447 average time/residue: 0.2827 time to fit residues: 190.0375 Evaluate side-chains 451 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 383 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 0.0670 chunk 118 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 5 GLN E 3 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17889 Z= 0.199 Angle : 0.668 8.937 24207 Z= 0.350 Chirality : 0.046 0.386 2615 Planarity : 0.005 0.056 3063 Dihedral : 5.214 55.322 2517 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 3.95 % Allowed : 20.23 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2185 helix: -4.85 (0.34), residues: 6 sheet: -0.07 (0.17), residues: 936 loop : -1.43 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 35A HIS 0.006 0.001 HIS D 173 PHE 0.012 0.001 PHE E 100E TYR 0.028 0.001 TYR C 206 ARG 0.006 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 404 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.5070 (t) cc_final: 0.4847 (t) REVERT: A 134 HIS cc_start: 0.6898 (t70) cc_final: 0.6491 (t-170) REVERT: J 100 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.4899 (t80) REVERT: E 16 GLU cc_start: 0.7960 (pt0) cc_final: 0.7693 (pt0) REVERT: E 100 PHE cc_start: 0.4116 (OUTLIER) cc_final: 0.3497 (t80) REVERT: C 360 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7346 (ptmt) outliers start: 75 outliers final: 61 residues processed: 444 average time/residue: 0.3036 time to fit residues: 204.4491 Evaluate side-chains 444 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 381 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 5 GLN E 3 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN D 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17889 Z= 0.234 Angle : 0.686 9.433 24207 Z= 0.360 Chirality : 0.046 0.380 2615 Planarity : 0.005 0.055 3063 Dihedral : 5.205 54.516 2516 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 4.00 % Allowed : 20.39 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.28 (0.18), residues: 2185 helix: -4.85 (0.34), residues: 6 sheet: -0.08 (0.17), residues: 941 loop : -1.48 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 188 HIS 0.006 0.001 HIS D 173 PHE 0.022 0.002 PHE F 98 TYR 0.027 0.001 TYR C 206 ARG 0.005 0.000 ARG B 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 388 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.5234 (t) cc_final: 0.4939 (t) REVERT: A 134 HIS cc_start: 0.6872 (t70) cc_final: 0.6465 (t-170) REVERT: J 100 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.4937 (t80) REVERT: E 16 GLU cc_start: 0.7993 (pt0) cc_final: 0.7728 (pt0) REVERT: E 100 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3362 (t80) REVERT: B 358 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8846 (tppt) REVERT: C 134 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6740 (m-70) REVERT: C 360 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7436 (ptmt) REVERT: C 449 MET cc_start: 0.6875 (ptp) cc_final: 0.6660 (ptp) outliers start: 76 outliers final: 64 residues processed: 430 average time/residue: 0.2905 time to fit residues: 187.4065 Evaluate side-chains 444 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 377 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 178 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN E 3 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.170559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.147336 restraints weight = 24222.361| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.67 r_work: 0.4251 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 17889 Z= 0.356 Angle : 0.876 59.199 24207 Z= 0.484 Chirality : 0.049 0.921 2615 Planarity : 0.005 0.055 3063 Dihedral : 5.193 54.480 2516 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 3.95 % Allowed : 20.50 % Favored : 75.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.41 % 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: -1.28 (0.18), residues: 2185 helix: -4.85 (0.34), residues: 6 sheet: -0.08 (0.17), residues: 941 loop : -1.48 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 188 HIS 0.006 0.001 HIS D 173 PHE 0.018 0.002 PHE F 98 TYR 0.036 0.002 TYR D 210 ARG 0.005 0.000 ARG K 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5021.45 seconds wall clock time: 89 minutes 49.11 seconds (5389.11 seconds total)