Starting phenix.real_space_refine on Tue Aug 6 19:01:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/08_2024/8u1s_41826.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/08_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_41826/08_2024/8u1s_41826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/08_2024/8u1s_41826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/08_2024/8u1s_41826.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1s_41826/08_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-5409/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: 10.11, 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: 6.17 Conformation dependent library (CDL) restraints added in 3.3 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: 2.63 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: 6.00 Time building geometry restraints manager: 6.85 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 3.120 nonbonded pdb=" NE ARG A 252 " pdb=" OE2 GLU A 264 " model vdw 1.548 3.120 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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.750 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.730 ------------------------------------------------------------------------------- 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 : 1.922 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: 0.3284 time to fit residues: 325.2531 Evaluate side-chains 421 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 413 time to evaluate : 1.812 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 230 ASN A 235 ASN J 3 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 57 ASN E 3 GLN F 79 GLN B 235 ASN B 329 ASN C 169 ASN C 220 ASN C 230 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 17889 Z= 0.302 Angle : 0.843 10.602 24207 Z= 0.458 Chirality : 0.051 0.295 2615 Planarity : 0.005 0.045 3063 Dihedral : 6.922 59.532 2529 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.35 % Favored : 94.00 % Rotamer: Outliers : 3.32 % Allowed : 11.38 % Favored : 85.30 % 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: -0.67 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.37 (0.16), residues: 911 loop : -1.05 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 408 HIS 0.010 0.002 HIS D 173 PHE 0.023 0.002 PHE G 100E TYR 0.028 0.002 TYR K 91 ARG 0.010 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 558 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 495 time to evaluate : 1.980 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: A 134 HIS cc_start: 0.7444 (t70) cc_final: 0.7094 (t-170) REVERT: A 241 THR cc_start: 0.8077 (t) cc_final: 0.7635 (m) REVERT: J 32 THR cc_start: 0.7835 (p) cc_final: 0.7414 (t) REVERT: I 27 GLN cc_start: 0.8381 (mt0) cc_final: 0.8100 (mt0) REVERT: F 82 ASP cc_start: 0.7580 (m-30) cc_final: 0.7214 (m-30) REVERT: B 295 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7365 (tpp-160) REVERT: C 116 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6765 (mmm160) REVERT: C 117 GLU cc_start: 0.7780 (mp0) cc_final: 0.7215 (mp0) REVERT: D 132 LEU cc_start: 0.8479 (mt) cc_final: 0.8227 (mp) REVERT: D 215 HIS cc_start: 0.7199 (m-70) cc_final: 0.6843 (m90) REVERT: D 333 ILE cc_start: 0.5307 (OUTLIER) cc_final: 0.4955 (pt) REVERT: D 338 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6534 (tm-30) outliers start: 63 outliers final: 36 residues processed: 529 average time/residue: 0.3076 time to fit residues: 243.9488 Evaluate side-chains 457 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 419 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 320 ASP 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 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER 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 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 178 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 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 0.0010 chunk 165 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN J 5 GLN K 79 GLN G 3 GLN I 79 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN B 220 ASN C 169 ASN D 230 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17889 Z= 0.279 Angle : 0.751 7.835 24207 Z= 0.404 Chirality : 0.048 0.201 2615 Planarity : 0.005 0.049 3063 Dihedral : 6.399 58.774 2525 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.45 % Favored : 94.10 % Rotamer: Outliers : 3.64 % Allowed : 14.59 % Favored : 81.77 % 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: -0.85 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.26 (0.17), residues: 916 loop : -1.21 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 388 HIS 0.010 0.002 HIS D 173 PHE 0.028 0.002 PHE E 100E TYR 0.025 0.002 TYR L 94 ARG 0.009 0.001 ARG D 300 *********************** 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 528 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 459 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6969 (tm-30) REVERT: A 134 HIS cc_start: 0.7418 (t70) cc_final: 0.7021 (t-170) REVERT: A 418 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8440 (mttm) REVERT: J 32 THR cc_start: 0.7867 (p) cc_final: 0.7405 (t) REVERT: K 18 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8042 (ttm170) REVERT: I 27 GLN cc_start: 0.8423 (mt0) cc_final: 0.8141 (mt0) REVERT: F 82 ASP cc_start: 0.7550 (m-30) cc_final: 0.7264 (m-30) REVERT: B 295 ARG cc_start: 0.7769 (tpp-160) cc_final: 0.7435 (tpp-160) REVERT: C 117 GLU cc_start: 0.7739 (mp0) cc_final: 0.7207 (mp0) REVERT: C 424 CYS cc_start: 0.5693 (m) cc_final: 0.5419 (m) REVERT: D 215 HIS cc_start: 0.7115 (m-70) cc_final: 0.6802 (m90) REVERT: D 333 ILE cc_start: 0.5319 (OUTLIER) cc_final: 0.5057 (pt) outliers start: 69 outliers final: 49 residues processed: 494 average time/residue: 0.3040 time to fit residues: 222.3527 Evaluate side-chains 447 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 396 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 A residue 359 SER Chi-restraints excluded: chain A residue 418 LYS 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 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 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 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 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 213 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 222 LEU 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: 6.9990 chunk 149 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN G 3 GLN I 90 GLN I 100 GLN E 3 GLN C 219 ASN D 235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17889 Z= 0.285 Angle : 0.719 7.960 24207 Z= 0.385 Chirality : 0.048 0.208 2615 Planarity : 0.005 0.089 3063 Dihedral : 6.013 57.870 2522 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.13 % Favored : 93.41 % Rotamer: Outliers : 4.37 % Allowed : 14.75 % Favored : 80.87 % 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: -1.01 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.15 (0.17), residues: 911 loop : -1.31 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 177 HIS 0.009 0.002 HIS D 173 PHE 0.020 0.002 PHE E 100E TYR 0.022 0.002 TYR L 94 ARG 0.009 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 519 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 436 time to evaluate : 2.029 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: 0.7302 (t70) cc_final: 0.6871 (t-170) REVERT: A 418 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (mttm) REVERT: J 32 THR cc_start: 0.8010 (p) cc_final: 0.7520 (t) REVERT: G 34 TYR cc_start: 0.8306 (m-80) cc_final: 0.8074 (m-80) REVERT: F 82 ASP cc_start: 0.7526 (m-30) cc_final: 0.7219 (m-30) REVERT: B 134 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7232 (m90) REVERT: B 295 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7439 (tpp-160) REVERT: C 117 GLU cc_start: 0.7767 (mp0) cc_final: 0.7197 (mp0) REVERT: C 405 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: D 215 HIS cc_start: 0.7103 (m-70) cc_final: 0.6801 (m90) REVERT: D 333 ILE cc_start: 0.5348 (OUTLIER) cc_final: 0.5147 (pt) outliers start: 83 outliers final: 60 residues processed: 473 average time/residue: 0.2957 time to fit residues: 207.8373 Evaluate side-chains 464 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 399 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 421 ASP 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 30 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 54 LEU 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 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 23 THR 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 F residue 97 THR 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 L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR 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 193 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 405 GLU 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 319 THR Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** J 5 GLN G 3 GLN I 100 GLN B 230 ASN C 169 ASN C 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 17889 Z= 0.433 Angle : 0.786 7.864 24207 Z= 0.419 Chirality : 0.050 0.218 2615 Planarity : 0.006 0.063 3063 Dihedral : 6.034 58.994 2521 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.09 % Favored : 92.49 % Rotamer: Outliers : 5.06 % Allowed : 15.70 % Favored : 79.24 % 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: -1.40 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.13 (0.17), residues: 893 loop : -1.56 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 32 HIS 0.011 0.002 HIS D 173 PHE 0.025 0.003 PHE E 100E TYR 0.027 0.002 TYR L 94 ARG 0.012 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 508 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 412 time to evaluate : 2.012 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: 0.7174 (t70) cc_final: 0.6772 (t-170) REVERT: A 418 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8537 (mttm) REVERT: G 57 ASN cc_start: 0.8313 (p0) cc_final: 0.8000 (p0) REVERT: E 100 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.4276 (t80) REVERT: H 100 TRP cc_start: 0.7841 (m100) cc_final: 0.7615 (m-10) REVERT: B 134 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7229 (m90) REVERT: B 295 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7510 (tpp-160) REVERT: C 117 GLU cc_start: 0.7785 (mp0) cc_final: 0.7349 (mp0) REVERT: C 449 MET cc_start: 0.7366 (ptp) cc_final: 0.6979 (ptp) REVERT: D 215 HIS cc_start: 0.7318 (m-70) cc_final: 0.6853 (m90) REVERT: D 220 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.7001 (t0) REVERT: D 333 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.5194 (pt) REVERT: D 348 ILE cc_start: 0.8226 (tp) cc_final: 0.7975 (tt) outliers start: 96 outliers final: 67 residues processed: 453 average time/residue: 0.2926 time to fit residues: 197.5630 Evaluate side-chains 455 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 382 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 229 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 418 LYS 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 54 LEU 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 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 23 THR 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 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 98 HIS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 31 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 B residue 134 HIS Chi-restraints excluded: chain B residue 166 THR 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 295 ARG Chi-restraints excluded: chain B residue 334 THR 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 169 ASN 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 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 220 ASN 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 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN C 134 HIS C 169 ASN C 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17889 Z= 0.244 Angle : 0.707 8.827 24207 Z= 0.374 Chirality : 0.047 0.211 2615 Planarity : 0.005 0.066 3063 Dihedral : 5.726 58.360 2521 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.64 % Favored : 93.04 % Rotamer: Outliers : 4.43 % Allowed : 17.02 % Favored : 78.56 % 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: -1.39 (0.17), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.12 (0.17), residues: 901 loop : -1.55 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 35 HIS 0.006 0.002 HIS A 354 PHE 0.015 0.002 PHE E 100E TYR 0.025 0.002 TYR L 94 ARG 0.007 0.001 ARG D 300 *********************** 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 520 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 436 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.7016 (t70) cc_final: 0.6678 (t-170) REVERT: A 418 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8431 (mttm) REVERT: G 100 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5637 (t80) REVERT: E 5 GLN cc_start: 0.8061 (mp-120) cc_final: 0.7604 (mp10) REVERT: E 100 PHE cc_start: 0.4929 (OUTLIER) cc_final: 0.4132 (t80) REVERT: B 134 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7201 (m90) REVERT: B 295 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7432 (tpp-160) REVERT: B 369 MET cc_start: 0.8419 (mmm) cc_final: 0.8026 (mmp) REVERT: C 117 GLU cc_start: 0.7807 (mp0) cc_final: 0.7231 (mp0) REVERT: C 403 MET cc_start: 0.7624 (mtm) cc_final: 0.7267 (mpp) outliers start: 84 outliers final: 59 residues processed: 475 average time/residue: 0.2958 time to fit residues: 210.5492 Evaluate side-chains 451 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 387 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 418 LYS 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 79 SER Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 54 LEU 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 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 100 PHE 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 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 23 THR 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 74 THR Chi-restraints excluded: chain F residue 75 ILE 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 L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 134 HIS 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 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR 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 334 THR Chi-restraints excluded: chain C residue 405 GLU 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 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN C 169 ASN C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17889 Z= 0.237 Angle : 0.710 9.452 24207 Z= 0.374 Chirality : 0.047 0.206 2615 Planarity : 0.005 0.059 3063 Dihedral : 5.552 57.920 2519 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 4.69 % Allowed : 17.60 % Favored : 77.71 % 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: -1.46 (0.17), residues: 2185 helix: -4.86 (0.34), residues: 6 sheet: -0.22 (0.17), residues: 923 loop : -1.58 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 35 HIS 0.012 0.002 HIS C 134 PHE 0.020 0.002 PHE K 62 TYR 0.031 0.002 TYR L 94 ARG 0.006 0.001 ARG D 300 *********************** 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 496 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 407 time to evaluate : 1.732 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: 0.6990 (t70) cc_final: 0.6675 (t-170) REVERT: A 418 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8423 (mttm) REVERT: A 429 MET cc_start: 0.7138 (mtt) cc_final: 0.6821 (mtt) REVERT: J 100 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.4718 (t80) REVERT: G 100 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5544 (t80) REVERT: E 100 PHE cc_start: 0.4831 (OUTLIER) cc_final: 0.3996 (t80) REVERT: B 134 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7184 (m90) REVERT: B 295 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7479 (tpp-160) REVERT: B 369 MET cc_start: 0.8376 (mmm) cc_final: 0.7970 (mmp) REVERT: C 79 GLU cc_start: 0.7676 (tp30) cc_final: 0.7155 (mt-10) REVERT: C 117 GLU cc_start: 0.7765 (mp0) cc_final: 0.7230 (mp0) REVERT: C 327 ARG cc_start: 0.7190 (ptt-90) cc_final: 0.6929 (ptt-90) REVERT: D 215 HIS cc_start: 0.7213 (m-70) cc_final: 0.6897 (m90) outliers start: 89 outliers final: 67 residues processed: 450 average time/residue: 0.2918 time to fit residues: 196.4886 Evaluate side-chains 461 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 388 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 LYS 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 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 22 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 54 LEU 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 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 PHE 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 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 23 THR 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 100 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 93 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG 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 193 VAL Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 405 GLU 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 295 ARG 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: 0.6980 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 ASN C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17889 Z= 0.252 Angle : 0.711 10.482 24207 Z= 0.375 Chirality : 0.048 0.514 2615 Planarity : 0.005 0.059 3063 Dihedral : 5.484 57.120 2519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 4.32 % Allowed : 18.44 % Favored : 77.24 % 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: -1.48 (0.17), residues: 2185 helix: -4.85 (0.34), residues: 6 sheet: -0.24 (0.17), residues: 919 loop : -1.58 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 35 HIS 0.005 0.002 HIS D 173 PHE 0.015 0.002 PHE E 100E TYR 0.029 0.002 TYR L 94 ARG 0.007 0.000 ARG D 300 *********************** 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 481 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 399 time to evaluate : 2.093 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: 0.6933 (t70) cc_final: 0.6613 (t-170) REVERT: A 418 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8489 (mttm) REVERT: A 429 MET cc_start: 0.7146 (mtt) cc_final: 0.6759 (mtt) REVERT: J 100 PHE cc_start: 0.6110 (OUTLIER) cc_final: 0.4603 (t80) REVERT: K 65 SER cc_start: 0.7962 (t) cc_final: 0.7749 (p) REVERT: G 100 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5558 (t80) REVERT: E 100 PHE cc_start: 0.4759 (OUTLIER) cc_final: 0.3890 (t80) REVERT: B 134 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7211 (m90) REVERT: B 369 MET cc_start: 0.8373 (mmm) cc_final: 0.7935 (mmp) REVERT: C 117 GLU cc_start: 0.7776 (mp0) cc_final: 0.7240 (mp0) REVERT: C 327 ARG cc_start: 0.7234 (ptt-90) cc_final: 0.6999 (ptt-90) outliers start: 82 outliers final: 62 residues processed: 439 average time/residue: 0.2870 time to fit residues: 189.7978 Evaluate side-chains 450 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 383 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 LYS 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 79 SER Chi-restraints excluded: chain J residue 100 PHE 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 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 23 THR 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 100 PHE 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 E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 THR 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 19 VAL Chi-restraints excluded: chain F residue 42 GLU 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 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 93 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 405 GLU 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 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: 5.9990 chunk 202 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 85 optimal weight: 0.0030 chunk 154 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN G 5 GLN C 155 HIS C 169 ASN C 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17889 Z= 0.244 Angle : 0.706 10.208 24207 Z= 0.373 Chirality : 0.048 0.493 2615 Planarity : 0.005 0.060 3063 Dihedral : 5.401 56.285 2518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 4.06 % Allowed : 19.18 % Favored : 76.77 % 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: -1.48 (0.17), residues: 2185 helix: -4.85 (0.34), residues: 6 sheet: -0.26 (0.17), residues: 924 loop : -1.56 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.005 0.001 HIS D 173 PHE 0.015 0.002 PHE E 100E TYR 0.028 0.002 TYR L 94 ARG 0.007 0.001 ARG D 300 *********************** 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 476 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 399 time to evaluate : 1.954 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: 0.6864 (t70) cc_final: 0.6557 (t-170) REVERT: J 100 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.4744 (t80) REVERT: K 65 SER cc_start: 0.7919 (t) cc_final: 0.7717 (p) REVERT: G 100 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5551 (t80) REVERT: E 100 PHE cc_start: 0.4679 (OUTLIER) cc_final: 0.3911 (t80) REVERT: H 100 TRP cc_start: 0.7764 (m100) cc_final: 0.7549 (m-10) REVERT: B 134 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7192 (m90) REVERT: B 295 ARG cc_start: 0.7651 (tpp-160) cc_final: 0.7432 (tpm170) REVERT: B 369 MET cc_start: 0.8326 (mmm) cc_final: 0.7912 (mmp) REVERT: B 449 MET cc_start: 0.7313 (ptp) cc_final: 0.6999 (ptt) REVERT: C 79 GLU cc_start: 0.7761 (tp30) cc_final: 0.7145 (mt-10) REVERT: C 117 GLU cc_start: 0.7801 (mp0) cc_final: 0.7272 (mp0) REVERT: C 418 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8380 (mmtp) outliers start: 77 outliers final: 59 residues processed: 440 average time/residue: 0.2907 time to fit residues: 191.2418 Evaluate side-chains 445 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 382 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS 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 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS 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 J residue 100 PHE 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 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain G residue 23 THR 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 100 PHE 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 E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 THR 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 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 L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR 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 249 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 405 GLU 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 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 207 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 ASN C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17889 Z= 0.333 Angle : 0.762 10.421 24207 Z= 0.402 Chirality : 0.049 0.485 2615 Planarity : 0.006 0.122 3063 Dihedral : 5.557 54.933 2517 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.60 % Favored : 92.08 % Rotamer: Outliers : 3.74 % Allowed : 19.60 % Favored : 76.66 % 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: -1.58 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.35 (0.17), residues: 926 loop : -1.62 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 35A HIS 0.008 0.002 HIS D 173 PHE 0.018 0.002 PHE E 100E TYR 0.029 0.002 TYR L 94 ARG 0.013 0.001 ARG C 327 ********************** 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: 71 poor density : 393 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.6827 (t70) cc_final: 0.6351 (t-170) REVERT: J 100 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.4934 (t80) REVERT: K 65 SER cc_start: 0.7948 (t) cc_final: 0.7734 (p) REVERT: G 100 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5562 (t80) REVERT: E 100 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.3966 (t80) REVERT: H 100 TRP cc_start: 0.7811 (m100) cc_final: 0.7585 (m-10) REVERT: B 134 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7219 (m90) REVERT: B 295 ARG cc_start: 0.7701 (tpp-160) cc_final: 0.7498 (tpm170) REVERT: C 117 GLU cc_start: 0.7824 (mp0) cc_final: 0.7288 (mp0) REVERT: C 418 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8392 (mmtp) outliers start: 71 outliers final: 60 residues processed: 428 average time/residue: 0.2929 time to fit residues: 188.5599 Evaluate side-chains 444 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 380 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS 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 J residue 100 PHE 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 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain G residue 23 THR 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 100 PHE 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 E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 THR 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 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 L residue 22 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 405 GLU 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 271 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.167208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.143879 restraints weight = 24334.278| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.65 r_work: 0.4225 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17889 Z= 0.263 Angle : 0.734 10.202 24207 Z= 0.387 Chirality : 0.048 0.474 2615 Planarity : 0.006 0.117 3063 Dihedral : 5.485 54.446 2517 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.19 % Favored : 92.49 % Rotamer: Outliers : 3.69 % Allowed : 20.44 % Favored : 75.87 % 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: -1.56 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.36 (0.17), residues: 937 loop : -1.59 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 35A HIS 0.005 0.001 HIS D 173 PHE 0.019 0.002 PHE F 98 TYR 0.028 0.002 TYR L 94 ARG 0.013 0.001 ARG C 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4785.62 seconds wall clock time: 85 minutes 36.13 seconds (5136.13 seconds total)