Starting phenix.real_space_refine on Tue Nov 19 07:41:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1q_41824/11_2024/8u1q_41824.cif" } resolution = 3.36 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= 0.059 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 136 5.16 5 C 11972 2.51 5 N 3228 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2994 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 18, 'TRANS': 368} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Restraints were copied for chains: J, L, O, C, G, M, I, H, N, F, K, P Time building chain proxies: 8.66, per 1000 atoms: 0.46 Number of scatterers: 19016 At special positions: 0 Unit cell: (185.15, 185.15, 69, 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 136 16.00 O 3680 8.00 N 3228 7.00 C 11972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.06 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=1.41 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=2.02 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG B 1 " - " ASN A 284 " " NAG F 1 " - " ASN C 284 " " NAG K 1 " - " ASN G 284 " " NAG P 1 " - " ASN M 284 " Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 44 sheets defined 2.3% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing sheet with id=1, first strand: chain 'A' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE A 445 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU A 97 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 443 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 440 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 428 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A 409 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 174 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 158 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE A 172 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER A 178 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 202 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 204 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=5, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU A 250 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 286 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE A 281 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 288 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS A 279 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 290 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS A 277 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET A 375 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET A 377 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 381 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE A 396 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE C 445 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 97 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 443 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 440 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 428 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR C 409 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER C 178 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 222 through 224 Processing sheet with id=16, first strand: chain 'C' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU C 250 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR C 286 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C 281 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU C 288 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA C 290 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS C 277 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET C 375 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET C 377 " --> pdb=" O MET C 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 381 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 396 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=20, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP D 35A" --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER E 65 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE G 445 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU G 97 " --> pdb=" O THR G 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR G 443 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER G 440 " --> pdb=" O HIS G 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU G 428 " --> pdb=" O TYR G 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR G 409 " --> pdb=" O GLU G 428 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'G' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU G 113 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA G 136 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE G 115 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS G 134 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU G 117 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 132 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET G 174 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER G 158 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE G 172 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'G' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER G 178 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 202 " --> pdb=" O THR G 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR G 213 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 204 " --> pdb=" O THR G 211 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'G' and resid 222 through 224 Processing sheet with id=27, first strand: chain 'G' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU G 250 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG G 257 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE G 261 " --> pdb=" O ARG G 257 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR G 268 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU G 316 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR G 286 " --> pdb=" O PHE G 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE G 281 " --> pdb=" O THR G 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU G 288 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS G 279 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA G 290 " --> pdb=" O CYS G 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS G 277 " --> pdb=" O ALA G 290 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET G 375 " --> pdb=" O PRO G 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET G 377 " --> pdb=" O MET G 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL G 381 " --> pdb=" O PHE G 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE G 396 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=31, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP I 35A" --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN J 27 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER J 67 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE J 29 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER J 65 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE M 445 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU M 97 " --> pdb=" O THR M 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR M 443 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER M 440 " --> pdb=" O HIS M 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU M 428 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR M 409 " --> pdb=" O GLU M 428 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'M' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU M 113 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 136 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE M 115 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS M 134 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU M 117 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU M 132 " --> pdb=" O GLU M 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET M 174 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER M 158 " --> pdb=" O PHE M 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE M 172 " --> pdb=" O SER M 158 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU M 202 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR M 213 " --> pdb=" O LEU M 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL M 204 " --> pdb=" O THR M 211 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'M' and resid 222 through 224 Processing sheet with id=38, first strand: chain 'M' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR M 286 " --> pdb=" O PHE M 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE M 281 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU M 288 " --> pdb=" O CYS M 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS M 279 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA M 290 " --> pdb=" O CYS M 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS M 277 " --> pdb=" O ALA M 290 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET M 375 " --> pdb=" O PRO M 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET M 377 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL M 381 " --> pdb=" O PHE M 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE M 396 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=42, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER N 50 " --> pdb=" O TRP N 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP N 35A" --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN O 27 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER O 67 " --> pdb=" O GLN O 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE O 29 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER O 65 " --> pdb=" O ILE O 29 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1500 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: 6.79 Time building geometry restraints manager: 5.54 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: 3780 1.32 - 1.45: 6292 1.45 - 1.59: 9192 1.59 - 1.73: 40 1.73 - 1.86: 180 Bond restraints: 19484 Sorted by residual: bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS G 354 " pdb=" CG HIS G 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS M 354 " pdb=" CG HIS M 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" NE ARG C 327 " pdb=" CZ ARG C 327 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.10e-02 8.26e+03 3.31e+01 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 20708 2.06 - 4.13: 4360 4.13 - 6.19: 1028 6.19 - 8.26: 232 8.26 - 10.32: 60 Bond angle restraints: 26388 Sorted by residual: angle pdb=" C GLY G 335 " pdb=" N PRO G 336 " pdb=" CA PRO G 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY C 335 " pdb=" N PRO C 336 " pdb=" CA PRO C 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY M 335 " pdb=" N PRO M 336 " pdb=" CA PRO M 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta sigma weight residual 120.03 127.91 -7.88 9.90e-01 1.02e+00 6.34e+01 ... (remaining 26383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 11085 15.96 - 31.92: 348 31.92 - 47.88: 68 47.88 - 63.84: 54 63.84 - 79.80: 29 Dihedral angle restraints: 11584 sinusoidal: 4620 harmonic: 6964 Sorted by residual: dihedral pdb=" CB CYS A 182 " pdb=" SG CYS A 182 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -17.42 -68.58 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA THR C 325 " pdb=" C THR C 325 " pdb=" N PRO C 326 " pdb=" CA PRO C 326 " ideal model delta harmonic sigma weight residual 180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA THR G 325 " pdb=" C THR G 325 " pdb=" N PRO G 326 " pdb=" CA PRO G 326 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 11581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1968 0.099 - 0.198: 676 0.198 - 0.298: 164 0.298 - 0.397: 20 0.397 - 0.496: 12 Chirality restraints: 2840 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 ... (remaining 2837 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 52 " -0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR D 52 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 52 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 52 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 52 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 52 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 52 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 52 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 52 " 0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR H 52 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR H 52 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 52 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR H 52 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 52 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR H 52 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 52 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 52 " 0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR N 52 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR N 52 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR N 52 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR N 52 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 52 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR N 52 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 52 " 0.059 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 32 2.11 - 2.80: 4939 2.80 - 3.50: 23681 3.50 - 4.20: 50204 4.20 - 4.90: 81992 Nonbonded interactions: 160848 Sorted by model distance: nonbonded pdb=" SG CYS C 182 " pdb=" SG CYS C 229 " model vdw 1.407 3.760 nonbonded pdb=" SG CYS M 182 " pdb=" SG CYS M 229 " model vdw 1.407 3.760 nonbonded pdb=" SG CYS G 182 " pdb=" SG CYS G 229 " model vdw 1.407 3.760 nonbonded pdb=" SG CYS G 279 " pdb=" SG CYS G 289 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS C 279 " pdb=" SG CYS C 289 " model vdw 2.018 3.760 ... (remaining 160843 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' selection = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' selection = chain 'O' } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.800 Find NCS groups from input model: 0.710 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.021 0.163 19484 Z= 1.391 Angle : 1.926 10.323 26388 Z= 1.268 Chirality : 0.108 0.496 2840 Planarity : 0.010 0.088 3356 Dihedral : 10.357 79.802 7168 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.13 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 3.70 % 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: -0.75 (0.16), residues: 2424 helix: -4.87 (0.12), residues: 24 sheet: 0.18 (0.16), residues: 972 loop : -0.91 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.010 TRP C 456 HIS 0.017 0.003 HIS C 273 PHE 0.030 0.006 PHE E 98 TYR 0.072 0.009 TYR I 52 ARG 0.012 0.002 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 2.210 Fit side-chains REVERT: L 78 LEU cc_start: 0.7766 (tt) cc_final: 0.7563 (tt) REVERT: C 116 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7839 (mmm160) REVERT: E 78 LEU cc_start: 0.7765 (tt) cc_final: 0.7564 (tt) REVERT: G 116 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7841 (mmm160) REVERT: M 116 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7841 (mmm160) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3381 time to fit residues: 253.9620 Evaluate side-chains 299 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN H 77 GLN L 79 GLN C 230 ASN C 294 ASN C 439 HIS D 77 GLN G 294 ASN I 77 GLN M 294 ASN M 439 HIS N 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19484 Z= 0.278 Angle : 0.793 19.531 26388 Z= 0.419 Chirality : 0.050 0.170 2840 Planarity : 0.005 0.052 3356 Dihedral : 6.577 61.026 2844 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.40 % Favored : 94.10 % Rotamer: Outliers : 2.00 % Allowed : 7.46 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.11 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: 0.15 (0.17), residues: 912 loop : -1.37 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.018 0.002 HIS C 101 PHE 0.029 0.002 PHE O 83 TYR 0.023 0.002 TYR N 34 ARG 0.005 0.001 ARG M 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 369 time to evaluate : 2.114 Fit side-chains REVERT: A 242 ASP cc_start: 0.6652 (t0) cc_final: 0.6329 (t0) REVERT: L 78 LEU cc_start: 0.7751 (tt) cc_final: 0.7427 (tt) REVERT: C 242 ASP cc_start: 0.6664 (t0) cc_final: 0.6357 (t0) REVERT: E 78 LEU cc_start: 0.7752 (tt) cc_final: 0.7427 (tt) REVERT: G 242 ASP cc_start: 0.6654 (t0) cc_final: 0.6355 (t0) REVERT: M 242 ASP cc_start: 0.6662 (t0) cc_final: 0.6348 (t0) outliers start: 41 outliers final: 21 residues processed: 390 average time/residue: 0.3064 time to fit residues: 184.3593 Evaluate side-chains 325 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 0.0470 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 294 ASN H 39 GLN H 100AASN L 6 GLN C 294 ASN D 39 GLN D 100AASN E 6 GLN G 230 ASN G 294 ASN I 39 GLN I 100AASN J 6 GLN M 230 ASN M 294 ASN N 39 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19484 Z= 0.191 Angle : 0.760 34.635 26388 Z= 0.351 Chirality : 0.047 0.181 2840 Planarity : 0.005 0.057 3356 Dihedral : 6.004 57.644 2844 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.57 % Favored : 94.10 % Rotamer: Outliers : 2.39 % Allowed : 9.80 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: 0.07 (0.16), residues: 936 loop : -1.56 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 177 HIS 0.005 0.001 HIS A 101 PHE 0.025 0.002 PHE H 78 TYR 0.019 0.002 TYR I 53 ARG 0.005 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 375 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 242 ASP cc_start: 0.6522 (t0) cc_final: 0.6242 (t0) REVERT: A 308 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 333 ILE cc_start: 0.8084 (mt) cc_final: 0.7777 (mm) REVERT: L 37 GLN cc_start: 0.8223 (tt0) cc_final: 0.7823 (tp40) REVERT: L 78 LEU cc_start: 0.7614 (tt) cc_final: 0.7325 (tt) REVERT: L 86 TYR cc_start: 0.7087 (m-80) cc_final: 0.6466 (m-80) REVERT: L 103 LYS cc_start: 0.7929 (ptmt) cc_final: 0.7715 (ptmt) REVERT: C 242 ASP cc_start: 0.6537 (t0) cc_final: 0.6249 (t0) REVERT: C 308 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 333 ILE cc_start: 0.8105 (mt) cc_final: 0.7807 (mm) REVERT: E 37 GLN cc_start: 0.8224 (tt0) cc_final: 0.7824 (tp40) REVERT: E 78 LEU cc_start: 0.7615 (tt) cc_final: 0.7327 (tt) REVERT: E 86 TYR cc_start: 0.7079 (m-80) cc_final: 0.6469 (m-80) REVERT: E 103 LYS cc_start: 0.7932 (ptmt) cc_final: 0.7715 (ptmt) REVERT: G 242 ASP cc_start: 0.6536 (t0) cc_final: 0.6250 (t0) REVERT: G 308 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7968 (tm-30) REVERT: G 333 ILE cc_start: 0.8097 (mt) cc_final: 0.7802 (mm) REVERT: J 37 GLN cc_start: 0.8219 (tt0) cc_final: 0.7818 (tp40) REVERT: J 86 TYR cc_start: 0.7080 (m-80) cc_final: 0.6462 (m-80) REVERT: J 103 LYS cc_start: 0.7925 (ptmt) cc_final: 0.7710 (ptmt) REVERT: M 242 ASP cc_start: 0.6531 (t0) cc_final: 0.6246 (t0) REVERT: M 308 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7961 (tm-30) REVERT: M 333 ILE cc_start: 0.8102 (mt) cc_final: 0.7806 (mm) REVERT: O 37 GLN cc_start: 0.8223 (tt0) cc_final: 0.7824 (tp40) REVERT: O 86 TYR cc_start: 0.7082 (m-80) cc_final: 0.6465 (m-80) REVERT: O 103 LYS cc_start: 0.7926 (ptmt) cc_final: 0.7713 (ptmt) outliers start: 49 outliers final: 32 residues processed: 404 average time/residue: 0.3243 time to fit residues: 199.9875 Evaluate side-chains 359 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 294 ASN H 39 GLN H 100AASN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 100AASN I 39 GLN I 100AASN ** M 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 100AASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19484 Z= 0.379 Angle : 0.791 31.370 26388 Z= 0.378 Chirality : 0.050 0.198 2840 Planarity : 0.005 0.068 3356 Dihedral : 6.232 61.112 2844 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.68 % Favored : 92.99 % Rotamer: Outliers : 2.92 % Allowed : 12.04 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.77 (0.15), residues: 2424 helix: -3.34 (0.75), residues: 24 sheet: -0.30 (0.17), residues: 908 loop : -1.79 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 438 HIS 0.009 0.002 HIS A 101 PHE 0.025 0.003 PHE L 83 TYR 0.021 0.002 TYR A 143 ARG 0.005 0.001 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 342 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7714 (tm-30) REVERT: H 75 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7969 (pttp) REVERT: C 308 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 75 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (pttp) REVERT: G 308 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7706 (tm-30) REVERT: I 75 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (pttp) REVERT: M 308 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7701 (tm-30) REVERT: N 75 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7964 (pttp) outliers start: 60 outliers final: 33 residues processed: 381 average time/residue: 0.3342 time to fit residues: 192.1254 Evaluate side-chains 355 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 318 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 75 LYS Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 204 optimal weight: 0.0170 chunk 57 optimal weight: 0.8980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100AASN I 100AASN ** M 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19484 Z= 0.225 Angle : 0.760 35.324 26388 Z= 0.344 Chirality : 0.048 0.197 2840 Planarity : 0.005 0.066 3356 Dihedral : 5.961 58.386 2844 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.68 % Favored : 92.99 % Rotamer: Outliers : 2.73 % Allowed : 13.65 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2424 helix: -3.06 (0.85), residues: 24 sheet: -0.30 (0.17), residues: 916 loop : -1.90 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 177 HIS 0.006 0.001 HIS G 101 PHE 0.029 0.002 PHE D 78 TYR 0.018 0.002 TYR A 296 ARG 0.004 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 2.312 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7653 (tm-30) REVERT: H 5 GLN cc_start: 0.7320 (pt0) cc_final: 0.7054 (pt0) REVERT: C 308 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 5 GLN cc_start: 0.7314 (pt0) cc_final: 0.7052 (pt0) REVERT: G 308 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7643 (tm-30) REVERT: I 5 GLN cc_start: 0.7318 (pt0) cc_final: 0.7055 (pt0) REVERT: J 14 SER cc_start: 0.7583 (t) cc_final: 0.7323 (p) REVERT: M 308 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7647 (tm-30) REVERT: N 5 GLN cc_start: 0.7317 (pt0) cc_final: 0.7055 (pt0) REVERT: O 14 SER cc_start: 0.7578 (t) cc_final: 0.7316 (p) outliers start: 56 outliers final: 27 residues processed: 369 average time/residue: 0.3248 time to fit residues: 185.2141 Evaluate side-chains 350 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN H 100AASN L 38 GLN C 439 HIS D 100AASN E 38 GLN I 100AASN J 38 GLN ** M 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100AASN O 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19484 Z= 0.356 Angle : 0.787 33.665 26388 Z= 0.365 Chirality : 0.049 0.213 2840 Planarity : 0.005 0.069 3356 Dihedral : 6.138 60.133 2844 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.80 % Favored : 91.87 % Rotamer: Outliers : 2.73 % Allowed : 12.38 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.05 (0.15), residues: 2424 helix: -3.10 (0.85), residues: 24 sheet: -0.43 (0.17), residues: 908 loop : -2.04 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.008 0.002 HIS A 101 PHE 0.022 0.002 PHE N 78 TYR 0.019 0.002 TYR C 296 ARG 0.005 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 2.200 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 5 GLN cc_start: 0.7358 (pt0) cc_final: 0.7111 (pt0) REVERT: L 37 GLN cc_start: 0.8071 (tt0) cc_final: 0.7852 (tp40) REVERT: L 78 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7278 (tt) REVERT: C 308 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 5 GLN cc_start: 0.7356 (pt0) cc_final: 0.7110 (pt0) REVERT: E 37 GLN cc_start: 0.8068 (tt0) cc_final: 0.7859 (tp40) REVERT: E 78 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7268 (tt) REVERT: G 308 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7720 (tm-30) REVERT: I 5 GLN cc_start: 0.7358 (pt0) cc_final: 0.7110 (pt0) REVERT: J 14 SER cc_start: 0.7622 (t) cc_final: 0.7355 (p) REVERT: M 308 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7735 (tm-30) REVERT: N 5 GLN cc_start: 0.7359 (pt0) cc_final: 0.7114 (pt0) REVERT: O 14 SER cc_start: 0.7617 (t) cc_final: 0.7350 (p) REVERT: O 37 GLN cc_start: 0.8105 (tt0) cc_final: 0.7904 (tp40) outliers start: 56 outliers final: 43 residues processed: 359 average time/residue: 0.3063 time to fit residues: 170.8656 Evaluate side-chains 347 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN H 100AASN C 169 ASN D 100AASN I 100AASN M 169 ASN ** M 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19484 Z= 0.232 Angle : 0.756 35.658 26388 Z= 0.339 Chirality : 0.047 0.212 2840 Planarity : 0.005 0.065 3356 Dihedral : 5.869 57.342 2844 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.26 % Favored : 92.57 % Rotamer: Outliers : 2.24 % Allowed : 13.16 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.04 (0.15), residues: 2424 helix: None (None), residues: 0 sheet: -0.45 (0.16), residues: 916 loop : -2.04 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 177 HIS 0.006 0.001 HIS A 101 PHE 0.030 0.002 PHE O 83 TYR 0.015 0.002 TYR E 94 ARG 0.006 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 335 time to evaluate : 2.290 Fit side-chains revert: symmetry clash REVERT: L 78 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7221 (tt) REVERT: E 78 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7210 (tt) REVERT: J 14 SER cc_start: 0.7596 (t) cc_final: 0.7016 (p) REVERT: M 308 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7679 (tm-30) REVERT: O 14 SER cc_start: 0.7588 (t) cc_final: 0.7007 (p) outliers start: 46 outliers final: 30 residues processed: 360 average time/residue: 0.2989 time to fit residues: 168.3723 Evaluate side-chains 348 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 0.0000 chunk 206 optimal weight: 5.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN D 100AASN I 100AASN M 439 HIS N 100AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19484 Z= 0.317 Angle : 0.775 34.092 26388 Z= 0.355 Chirality : 0.048 0.403 2840 Planarity : 0.005 0.066 3356 Dihedral : 6.004 59.101 2844 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.16 % Favored : 90.51 % Rotamer: Outliers : 2.24 % Allowed : 13.21 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.17 (0.15), residues: 2424 helix: -2.87 (0.94), residues: 24 sheet: -0.56 (0.16), residues: 916 loop : -2.09 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 36 HIS 0.007 0.002 HIS A 101 PHE 0.027 0.002 PHE E 83 TYR 0.017 0.002 TYR D 96 ARG 0.006 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 2.381 Fit side-chains revert: symmetry clash REVERT: L 37 GLN cc_start: 0.7822 (tt0) cc_final: 0.7617 (tt0) REVERT: L 78 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7066 (tt) REVERT: E 78 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7053 (tt) REVERT: J 14 SER cc_start: 0.7597 (t) cc_final: 0.7279 (p) REVERT: O 14 SER cc_start: 0.7593 (t) cc_final: 0.7274 (p) outliers start: 46 outliers final: 37 residues processed: 356 average time/residue: 0.3031 time to fit residues: 170.3613 Evaluate side-chains 360 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100AASN I 100AASN J 38 GLN N 100AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19484 Z= 0.318 Angle : 0.780 33.929 26388 Z= 0.358 Chirality : 0.050 0.408 2840 Planarity : 0.005 0.067 3356 Dihedral : 6.001 59.401 2844 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.09 % Favored : 91.58 % Rotamer: Outliers : 2.24 % Allowed : 13.89 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.23 (0.16), residues: 2424 helix: -2.88 (0.92), residues: 24 sheet: -0.63 (0.17), residues: 920 loop : -2.12 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 36 HIS 0.007 0.002 HIS A 101 PHE 0.028 0.002 PHE E 83 TYR 0.016 0.002 TYR D 96 ARG 0.011 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 336 time to evaluate : 2.142 Fit side-chains revert: symmetry clash REVERT: L 78 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7142 (tt) REVERT: E 61 ARG cc_start: 0.6518 (ptt-90) cc_final: 0.6306 (ptt-90) REVERT: E 78 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7169 (tt) REVERT: E 86 TYR cc_start: 0.6607 (m-80) cc_final: 0.6394 (m-80) REVERT: J 14 SER cc_start: 0.7531 (t) cc_final: 0.7212 (p) REVERT: O 14 SER cc_start: 0.7517 (t) cc_final: 0.7196 (p) REVERT: O 61 ARG cc_start: 0.6784 (ptt-90) cc_final: 0.6564 (ptt-90) REVERT: O 86 TYR cc_start: 0.6594 (m-80) cc_final: 0.6387 (m-80) outliers start: 46 outliers final: 39 residues processed: 362 average time/residue: 0.2855 time to fit residues: 164.2854 Evaluate side-chains 372 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19484 Z= 0.445 Angle : 0.824 31.509 26388 Z= 0.393 Chirality : 0.053 0.486 2840 Planarity : 0.005 0.070 3356 Dihedral : 6.340 62.670 2844 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.03 % Favored : 90.64 % Rotamer: Outliers : 2.24 % Allowed : 13.60 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.46 (0.16), residues: 2424 helix: -3.04 (0.86), residues: 24 sheet: -0.88 (0.17), residues: 940 loop : -2.21 (0.14), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 438 HIS 0.009 0.002 HIS C 101 PHE 0.027 0.002 PHE E 83 TYR 0.020 0.002 TYR I 96 ARG 0.009 0.001 ARG E 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: A 286 THR cc_start: 0.9168 (t) cc_final: 0.8962 (m) REVERT: L 78 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7080 (tt) REVERT: L 86 TYR cc_start: 0.7042 (m-80) cc_final: 0.6736 (m-80) REVERT: E 61 ARG cc_start: 0.6884 (ptt-90) cc_final: 0.6659 (ptt-90) REVERT: E 78 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7053 (tt) REVERT: E 86 TYR cc_start: 0.7165 (m-80) cc_final: 0.6884 (m-80) REVERT: J 14 SER cc_start: 0.7637 (t) cc_final: 0.7290 (p) REVERT: O 14 SER cc_start: 0.7624 (t) cc_final: 0.7276 (p) REVERT: O 86 TYR cc_start: 0.7164 (m-80) cc_final: 0.6884 (m-80) outliers start: 46 outliers final: 43 residues processed: 357 average time/residue: 0.2854 time to fit residues: 161.6884 Evaluate side-chains 369 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.149378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127846 restraints weight = 25817.622| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.80 r_work: 0.3579 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19484 Z= 0.241 Angle : 0.775 34.933 26388 Z= 0.353 Chirality : 0.049 0.363 2840 Planarity : 0.005 0.066 3356 Dihedral : 5.974 58.748 2844 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.00 % Favored : 91.67 % Rotamer: Outliers : 2.00 % Allowed : 14.38 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.36 (0.16), residues: 2424 helix: -2.78 (0.95), residues: 24 sheet: -0.79 (0.17), residues: 936 loop : -2.16 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.006 0.001 HIS C 101 PHE 0.029 0.002 PHE E 83 TYR 0.016 0.002 TYR L 94 ARG 0.008 0.000 ARG E 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.81 seconds wall clock time: 83 minutes 58.30 seconds (5038.30 seconds total)