Starting phenix.real_space_refine on Sat Feb 24 09:50:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nad_24270/02_2024/7nad_24270.pdb" } resolution = 3.04 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 62 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 756 5.49 5 S 85 5.16 5 C 24289 2.51 5 N 7816 2.21 5 O 10176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 43123 Number of models: 1 Model: "" Number of chains: 27 Chain: "1" Number of atoms: 14914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 14914 Classifications: {'RNA': 697} Modifications used: {'rna2p_pur': 69, 'rna2p_pyr': 49, 'rna3p_pur': 315, 'rna3p_pyr': 264} Link IDs: {'rna2p': 118, 'rna3p': 578} Chain breaks: 13 Chain: "2" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1255 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 47} Chain breaks: 3 Chain: "5" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1061 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 2 Chain: "8" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "G" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 175 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2675 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "P" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 4 Chain: "R" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 3 Chain: "X" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "b" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 431 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 593 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 2 Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "m" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3302 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 385} Chain breaks: 3 Chain: "n" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "p" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2628 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "t" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 221 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "u" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 481 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "w" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2707 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 11 Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 212 Classifications: {'peptide': 27} Link IDs: {'PCIS': 1, 'TRANS': 25} Chain: "x" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4340 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27227 SG CYS g 44 98.783 85.978 120.304 1.00 6.36 S ATOM 27245 SG CYS g 47 96.771 83.954 117.842 1.00 5.81 S ATOM 27499 SG CYS g 81 94.964 86.469 120.063 1.00 6.44 S ATOM 27518 SG CYS g 84 96.252 83.432 121.654 1.00 5.43 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ILE m 445 " occ=0.74 ... (6 atoms not shown) pdb=" CD1 ILE m 445 " occ=0.74 residue: pdb=" N ILE m 466 " occ=0.64 ... (6 atoms not shown) pdb=" CD1 ILE m 466 " occ=0.64 residue: pdb=" N PRO m 484 " occ=0.79 ... (5 atoms not shown) pdb=" CD PRO m 484 " occ=0.79 residue: pdb=" N ASP m 485 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP m 485 " occ=0.85 residue: pdb=" N LYS m 529 " occ=0.59 ... (7 atoms not shown) pdb=" NZ LYS m 529 " occ=0.59 residue: pdb=" N ARG m 720 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG m 720 " occ=0.60 residue: pdb=" N SER w 29 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER w 29 " occ=0.50 residue: pdb=" N LEU w 138 " occ=0.50 ... (6 atoms not shown) pdb=" CD2 LEU w 138 " occ=0.50 Time building chain proxies: 21.82, per 1000 atoms: 0.51 Number of scatterers: 43123 At special positions: 0 Unit cell: (180.36, 177.12, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 85 16.00 P 756 15.00 O 10176 8.00 N 7816 7.00 C 24289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.28 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " Number of angles added : 6 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 30 sheets defined 44.5% alpha, 15.2% beta 227 base pairs and 370 stacking pairs defined. Time for finding SS restraints: 14.49 Creating SS restraints... Processing helix chain '5' and resid 32 through 42 removed outlier: 3.537A pdb=" N ARG 5 36 " --> pdb=" O ASP 5 32 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY 5 42 " --> pdb=" O ASP 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 93 removed outlier: 3.519A pdb=" N GLU 5 90 " --> pdb=" O LYS 5 86 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) Processing helix chain '5' and resid 164 through 180 Processing helix chain '5' and resid 217 through 230 Processing helix chain '8' and resid 5 through 15 Processing helix chain '8' and resid 15 through 35 removed outlier: 4.329A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 Processing helix chain '8' and resid 51 through 60 Processing helix chain 'G' and resid 47 through 52 removed outlier: 3.979A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.874A pdb=" N GLU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.512A pdb=" N LEU I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU I 167 " --> pdb=" O CYS I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.953A pdb=" N VAL I 182 " --> pdb=" O MET I 178 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing helix chain 'I' and resid 198 through 203 removed outlier: 4.082A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 236 Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 261 through 266 removed outlier: 5.372A pdb=" N SER I 264 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS I 265 " --> pdb=" O THR I 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 266 " --> pdb=" O ALA I 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 261 through 266' Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.867A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 305 Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.621A pdb=" N ILE I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 340 removed outlier: 3.531A pdb=" N LEU I 340 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.580A pdb=" N ARG I 366 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 421 removed outlier: 3.620A pdb=" N GLU I 386 " --> pdb=" O GLN I 382 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU I 400 " --> pdb=" O ALA I 396 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 437 Processing helix chain 'I' and resid 438 through 440 No H-bonds generated for 'chain 'I' and resid 438 through 440' Processing helix chain 'I' and resid 519 through 523 removed outlier: 3.657A pdb=" N ARG I 523 " --> pdb=" O ARG I 520 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 32 Processing helix chain 'P' and resid 84 through 90 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.732A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 162 removed outlier: 5.002A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 40 Processing helix chain 'U' and resid 42 through 46 removed outlier: 3.637A pdb=" N GLY U 45 " --> pdb=" O LYS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 80 removed outlier: 3.733A pdb=" N ASN X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 131 through 138 Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.918A pdb=" N LYS Z 93 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.588A pdb=" N PHE Z 101 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'b' and resid 490 through 511 removed outlier: 3.558A pdb=" N ALA b 494 " --> pdb=" O LYS b 490 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 removed outlier: 3.963A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.836A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 81 through 110 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'm' and resid 393 through 397 removed outlier: 3.502A pdb=" N ALA m 397 " --> pdb=" O ASP m 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 393 through 397' Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 418 through 423 removed outlier: 4.229A pdb=" N ARG m 423 " --> pdb=" O LYS m 420 " (cutoff:3.500A) Processing helix chain 'm' and resid 519 through 532 removed outlier: 4.015A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) Processing helix chain 'm' and resid 533 through 538 removed outlier: 3.539A pdb=" N THR m 538 " --> pdb=" O GLY m 535 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 584 Processing helix chain 'm' and resid 616 through 619 removed outlier: 3.620A pdb=" N THR m 619 " --> pdb=" O SER m 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 616 through 619' Processing helix chain 'n' and resid 10 through 15 removed outlier: 3.517A pdb=" N ASN n 14 " --> pdb=" O GLY n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 39 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 70 removed outlier: 3.690A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 551 through 556 Processing helix chain 'n' and resid 557 through 559 No H-bonds generated for 'chain 'n' and resid 557 through 559' Processing helix chain 'n' and resid 560 through 582 Processing helix chain 'p' and resid 237 through 241 Processing helix chain 'p' and resid 245 through 252 removed outlier: 4.101A pdb=" N ASP p 249 " --> pdb=" O ASP p 245 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE p 250 " --> pdb=" O PRO p 246 " (cutoff:3.500A) Processing helix chain 'p' and resid 258 through 267 Processing helix chain 'p' and resid 268 through 270 No H-bonds generated for 'chain 'p' and resid 268 through 270' Processing helix chain 't' and resid 25 through 37 Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 105 through 112 Processing helix chain 'u' and resid 114 through 129 Processing helix chain 'u' and resid 130 through 138 Processing helix chain 'w' and resid 28 through 40 removed outlier: 3.978A pdb=" N LYS w 32 " --> pdb=" O ARG w 28 " (cutoff:3.500A) Processing helix chain 'w' and resid 129 through 144 removed outlier: 3.933A pdb=" N PHE w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) Processing helix chain 'w' and resid 165 through 176 removed outlier: 4.228A pdb=" N LEU w 169 " --> pdb=" O ASP w 165 " (cutoff:3.500A) Processing helix chain 'w' and resid 209 through 213 Processing helix chain 'w' and resid 214 through 219 removed outlier: 3.701A pdb=" N PHE w 219 " --> pdb=" O PRO w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 348 through 388 removed outlier: 4.098A pdb=" N ILE w 352 " --> pdb=" O GLU w 348 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.504A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 419 through 425 Processing helix chain 'w' and resid 456 through 479 Processing helix chain 'w' and resid 481 through 491 removed outlier: 3.819A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG w 490 " --> pdb=" O ALA w 486 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 560 Processing helix chain 'w' and resid 638 through 652 Processing helix chain 'w' and resid 696 through 701 Processing helix chain 'x' and resid 15 through 26 Processing helix chain 'x' and resid 31 through 42 removed outlier: 3.528A pdb=" N ILE x 38 " --> pdb=" O GLN x 34 " (cutoff:3.500A) Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 56 through 72 Proline residue: x 64 - end of helix Processing helix chain 'x' and resid 92 through 108 Processing helix chain 'x' and resid 129 through 141 Processing helix chain 'x' and resid 148 through 158 Processing helix chain 'x' and resid 173 through 178 Processing helix chain 'x' and resid 182 through 193 removed outlier: 3.583A pdb=" N LYS x 188 " --> pdb=" O LYS x 184 " (cutoff:3.500A) Processing helix chain 'x' and resid 211 through 217 removed outlier: 3.700A pdb=" N PHE x 214 " --> pdb=" O SER x 211 " (cutoff:3.500A) Processing helix chain 'x' and resid 244 through 246 No H-bonds generated for 'chain 'x' and resid 244 through 246' Processing helix chain 'x' and resid 247 through 257 Processing helix chain 'x' and resid 270 through 287 Processing helix chain 'x' and resid 304 through 317 Processing helix chain 'x' and resid 353 through 358 Processing helix chain 'x' and resid 359 through 361 No H-bonds generated for 'chain 'x' and resid 359 through 361' Processing helix chain 'x' and resid 362 through 366 Processing helix chain 'x' and resid 378 through 389 removed outlier: 4.139A pdb=" N PHE x 382 " --> pdb=" O ARG x 378 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE x 383 " --> pdb=" O GLU x 379 " (cutoff:3.500A) Proline residue: x 384 - end of helix Processing helix chain 'x' and resid 406 through 416 Processing helix chain 'x' and resid 418 through 438 Processing helix chain 'x' and resid 451 through 459 Processing helix chain 'x' and resid 467 through 474 Processing helix chain 'x' and resid 502 through 515 removed outlier: 3.723A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU x 508 " --> pdb=" O LYS x 504 " (cutoff:3.500A) Processing helix chain 'x' and resid 515 through 533 Processing helix chain 'x' and resid 536 through 558 removed outlier: 3.814A pdb=" N LYS x 556 " --> pdb=" O LYS x 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 145 through 148 removed outlier: 6.840A pdb=" N ASP x 46 " --> pdb=" O VAL x 222 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE x 224 " --> pdb=" O ASP x 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL x 48 " --> pdb=" O ILE x 224 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL x 226 " --> pdb=" O VAL x 48 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP x 50 " --> pdb=" O VAL x 226 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL x 47 " --> pdb=" O LEU x 201 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER x 203 " --> pdb=" O VAL x 47 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL x 49 " --> pdb=" O SER x 203 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU x 87 " --> pdb=" O VAL x 170 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP x 172 " --> pdb=" O LEU x 87 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE x 89 " --> pdb=" O ASP x 172 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER x 86 " --> pdb=" O LEU x 145 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLY x 147 " --> pdb=" O SER x 86 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE x 88 " --> pdb=" O GLY x 147 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN x 120 " --> pdb=" O ILE x 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 127 through 129 Processing sheet with id=AA3, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'U' and resid 54 through 58 removed outlier: 7.977A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.812A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.669A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 22 through 25 removed outlier: 7.090A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 12 through 15 Processing sheet with id=AB2, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'k' and resid 3 through 4 removed outlier: 4.868A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 399 through 405 Processing sheet with id=AB5, first strand: chain 'm' and resid 428 through 433 removed outlier: 5.292A pdb=" N CYS m 429 " --> pdb=" O THR m 806 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR m 806 " --> pdb=" O CYS m 429 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR m 431 " --> pdb=" O LEU m 804 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 440 through 445 removed outlier: 3.587A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR m 460 " --> pdb=" O SER m 456 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU m 465 " --> pdb=" O GLU m 471 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU m 471 " --> pdb=" O GLU m 465 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 488 through 493 removed outlier: 3.925A pdb=" N ILE m 589 " --> pdb=" O LEU m 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'm' and resid 599 through 602 Processing sheet with id=AB9, first strand: chain 'm' and resid 642 through 647 removed outlier: 5.850A pdb=" N VAL m 662 " --> pdb=" O LYS m 675 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS m 675 " --> pdb=" O VAL m 662 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 683 through 688 Processing sheet with id=AC2, first strand: chain 'm' and resid 726 through 731 removed outlier: 3.546A pdb=" N SER m 728 " --> pdb=" O ALA m 741 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE m 747 " --> pdb=" O LYS m 769 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS m 769 " --> pdb=" O ILE m 747 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL m 749 " --> pdb=" O LEU m 767 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 96 through 100 removed outlier: 7.021A pdb=" N ILE p 451 " --> pdb=" O LEU p 97 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER p 99 " --> pdb=" O ILE p 449 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE p 449 " --> pdb=" O SER p 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 106 through 110 removed outlier: 3.556A pdb=" N SER p 108 " --> pdb=" O GLY p 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL p 127 " --> pdb=" O GLN p 139 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN p 139 " --> pdb=" O VAL p 127 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR p 129 " --> pdb=" O GLN p 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN p 137 " --> pdb=" O GLU p 196 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 147 through 154 removed outlier: 6.814A pdb=" N ALA p 161 " --> pdb=" O ARG p 148 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL p 150 " --> pdb=" O VAL p 159 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL p 159 " --> pdb=" O VAL p 150 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR p 152 " --> pdb=" O ARG p 157 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ARG p 157 " --> pdb=" O TYR p 152 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY p 162 " --> pdb=" O THR p 166 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR p 166 " --> pdb=" O GLY p 162 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS p 171 " --> pdb=" O THR p 200 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR p 200 " --> pdb=" O LYS p 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'p' and resid 211 through 216 Processing sheet with id=AC7, first strand: chain 'p' and resid 290 through 293 removed outlier: 3.558A pdb=" N SER p 307 " --> pdb=" O THR p 311 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR p 311 " --> pdb=" O SER p 307 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE p 312 " --> pdb=" O THR p 325 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR p 325 " --> pdb=" O ILE p 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'p' and resid 332 through 338 removed outlier: 4.176A pdb=" N HIS p 352 " --> pdb=" O SER p 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 378 through 383 removed outlier: 6.230A pdb=" N VAL p 400 " --> pdb=" O THR p 413 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR p 413 " --> pdb=" O VAL p 400 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL p 402 " --> pdb=" O MET p 411 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'w' and resid 156 through 161 removed outlier: 6.495A pdb=" N PHE w 202 " --> pdb=" O PHE w 177 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE w 177 " --> pdb=" O PHE w 202 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 16 through 18 removed outlier: 3.616A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'x' and resid 294 through 299 removed outlier: 6.364A pdb=" N LYS x 263 " --> pdb=" O LEU x 341 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE x 343 " --> pdb=" O LYS x 263 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE x 265 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N GLU x 394 " --> pdb=" O LEU x 236 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU x 238 " --> pdb=" O GLU x 394 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 572 hydrogen bonds 938 hydrogen bond angles 0 basepair planarities 227 basepair parallelities 370 stacking parallelities Total time for adding SS restraints: 28.91 Time building geometry restraints manager: 20.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9344 1.33 - 1.45: 13311 1.45 - 1.57: 21160 1.57 - 1.69: 1494 1.69 - 1.81: 141 Bond restraints: 45450 Sorted by residual: bond pdb=" O3' G 12121 " pdb=" P G 12122 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.07e+00 bond pdb=" O5' G 12123 " pdb=" C5' G 12123 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.57e+00 bond pdb=" CB PRO u 131 " pdb=" CG PRO u 131 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.51e+00 bond pdb=" CB GLU R 152 " pdb=" CG GLU R 152 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" O5' G 12122 " pdb=" C5' G 12122 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.03e+00 ... (remaining 45445 not shown) Histogram of bond angle deviations from ideal: 98.74 - 106.13: 4625 106.13 - 113.52: 26704 113.52 - 120.91: 20438 120.91 - 128.30: 11893 128.30 - 135.69: 1196 Bond angle restraints: 64856 Sorted by residual: angle pdb=" N ASN x 406 " pdb=" CA ASN x 406 " pdb=" C ASN x 406 " ideal model delta sigma weight residual 112.86 123.58 -10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" N SER p 101 " pdb=" CA SER p 101 " pdb=" C SER p 101 " ideal model delta sigma weight residual 110.41 117.58 -7.17 1.23e+00 6.61e-01 3.40e+01 angle pdb=" N ARG P 131 " pdb=" CA ARG P 131 " pdb=" C ARG P 131 " ideal model delta sigma weight residual 108.19 114.39 -6.20 1.29e+00 6.01e-01 2.31e+01 angle pdb=" N LYS d 65 " pdb=" CA LYS d 65 " pdb=" C LYS d 65 " ideal model delta sigma weight residual 111.28 116.45 -5.17 1.09e+00 8.42e-01 2.25e+01 angle pdb=" N THR p 311 " pdb=" CA THR p 311 " pdb=" C THR p 311 " ideal model delta sigma weight residual 109.50 116.40 -6.90 1.58e+00 4.01e-01 1.91e+01 ... (remaining 64851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 26755 35.98 - 71.96: 1781 71.96 - 107.94: 210 107.94 - 143.91: 2 143.91 - 179.89: 4 Dihedral angle restraints: 28752 sinusoidal: 18993 harmonic: 9759 Sorted by residual: dihedral pdb=" O4' U 11764 " pdb=" C1' U 11764 " pdb=" N1 U 11764 " pdb=" C2 U 11764 " ideal model delta sinusoidal sigma weight residual -128.00 51.89 -179.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 12318 " pdb=" C1' U 12318 " pdb=" N1 U 12318 " pdb=" C2 U 12318 " ideal model delta sinusoidal sigma weight residual -128.00 27.66 -155.66 1 1.70e+01 3.46e-03 6.35e+01 dihedral pdb=" O4' C 11631 " pdb=" C1' C 11631 " pdb=" N1 C 11631 " pdb=" C2 C 11631 " ideal model delta sinusoidal sigma weight residual -160.00 -74.21 -85.79 1 1.50e+01 4.44e-03 3.95e+01 ... (remaining 28749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7445 0.080 - 0.159: 424 0.159 - 0.239: 27 0.239 - 0.318: 1 0.318 - 0.398: 2 Chirality restraints: 7899 Sorted by residual: chirality pdb=" CA ASN x 406 " pdb=" N ASN x 406 " pdb=" C ASN x 406 " pdb=" CB ASN x 406 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CG LEU R 155 " pdb=" CB LEU R 155 " pdb=" CD1 LEU R 155 " pdb=" CD2 LEU R 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA THR p 311 " pdb=" N THR p 311 " pdb=" C THR p 311 " pdb=" CB THR p 311 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7896 not shown) Planarity restraints: 5385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 330 " 0.023 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C GLU I 330 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU I 330 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU I 331 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN u 130 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO u 131 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO u 131 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO u 131 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 11646 " -0.032 2.00e-02 2.50e+03 1.43e-02 6.14e+00 pdb=" N9 G 11646 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 11646 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 11646 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G 11646 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 11646 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 11646 " 0.004 2.00e-02 2.50e+03 ... (remaining 5382 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2163 2.71 - 3.26: 39223 3.26 - 3.80: 75280 3.80 - 4.35: 99717 4.35 - 4.90: 146210 Nonbonded interactions: 362593 Sorted by model distance: nonbonded pdb=" O2' G 11560 " pdb=" O4' G 11561 " model vdw 2.159 2.440 nonbonded pdb=" OP2 G 1 894 " pdb=" N2 G 1 894 " model vdw 2.166 2.520 nonbonded pdb=" OG SER p 217 " pdb=" OD1 ASN p 219 " model vdw 2.203 2.440 nonbonded pdb=" O2' C 11657 " pdb=" O2' G 11796 " model vdw 2.203 2.440 nonbonded pdb=" OG SER p 122 " pdb=" OD1 ASP p 124 " model vdw 2.210 2.440 ... (remaining 362588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.17 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.040 Extract box with map and model: 18.350 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 132.680 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.002 0.079 45450 Z= 0.150 Angle : 0.517 10.716 64856 Z= 0.283 Chirality : 0.038 0.398 7899 Planarity : 0.004 0.101 5385 Dihedral : 19.893 179.893 22374 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.34 % Allowed : 1.24 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.96 (0.15), residues: 3220 helix: 1.77 (0.15), residues: 1347 sheet: 0.37 (0.22), residues: 571 loop : -0.40 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 PHE 0.024 0.001 PHE x 61 TYR 0.014 0.001 TYR c 23 ARG 0.009 0.000 ARG 5 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 349 time to evaluate : 3.735 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.7416 (mtt) cc_final: 0.7069 (mtt) REVERT: b 521 ARG cc_start: 0.8463 (mtt90) cc_final: 0.8038 (mtt90) REVERT: j 28 HIS cc_start: 0.7745 (t-90) cc_final: 0.7442 (t-170) REVERT: x 500 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5502 (t80) outliers start: 10 outliers final: 4 residues processed: 359 average time/residue: 0.6497 time to fit residues: 364.7053 Evaluate side-chains 286 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 281 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 9.9990 chunk 299 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 ASN I 382 GLN p 137 GLN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45450 Z= 0.256 Angle : 0.534 9.339 64856 Z= 0.279 Chirality : 0.038 0.264 7899 Planarity : 0.004 0.062 5385 Dihedral : 21.145 179.005 15359 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.11 % Allowed : 6.19 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3220 helix: 1.87 (0.14), residues: 1362 sheet: 0.23 (0.22), residues: 591 loop : -0.39 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 464 HIS 0.008 0.001 HIS p 310 PHE 0.024 0.002 PHE x 61 TYR 0.014 0.002 TYR m 608 ARG 0.008 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 3.624 Fit side-chains revert: symmetry clash REVERT: n 27 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7832 (m) REVERT: u 122 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5874 (ttp-170) REVERT: x 500 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5523 (t80) outliers start: 33 outliers final: 19 residues processed: 308 average time/residue: 0.6254 time to fit residues: 309.3678 Evaluate side-chains 298 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 276 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain m residue 407 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain u residue 136 ILE Chi-restraints excluded: chain w residue 542 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 388 optimal weight: 0.8980 chunk 320 optimal weight: 7.9990 chunk 356 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 288 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: Z 106 GLN w 137 GLN j 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 45450 Z= 0.133 Angle : 0.467 9.868 64856 Z= 0.245 Chirality : 0.035 0.239 7899 Planarity : 0.003 0.047 5385 Dihedral : 21.064 179.971 15359 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 8.27 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3220 helix: 2.07 (0.14), residues: 1367 sheet: 0.41 (0.22), residues: 597 loop : -0.39 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.022 0.001 PHE x 61 TYR 0.020 0.001 TYR p 96 ARG 0.008 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 283 time to evaluate : 3.689 Fit side-chains revert: symmetry clash REVERT: u 122 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5845 (ttp-170) REVERT: j 14 LYS cc_start: 0.6698 (mmtm) cc_final: 0.6168 (mppt) REVERT: x 500 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5458 (t80) outliers start: 31 outliers final: 19 residues processed: 298 average time/residue: 0.5983 time to fit residues: 284.3293 Evaluate side-chains 291 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 270 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 171 optimal weight: 0.0060 chunk 241 optimal weight: 6.9990 chunk 360 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 341 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 155 ASN j 16 HIS x 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 45450 Z= 0.116 Angle : 0.447 8.910 64856 Z= 0.235 Chirality : 0.034 0.222 7899 Planarity : 0.003 0.045 5385 Dihedral : 21.000 179.383 15356 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.24 % Allowed : 9.18 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 3220 helix: 2.22 (0.14), residues: 1369 sheet: 0.51 (0.22), residues: 585 loop : -0.33 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.023 0.001 PHE u 120 TYR 0.021 0.001 TYR p 238 ARG 0.008 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 281 time to evaluate : 3.906 Fit side-chains revert: symmetry clash REVERT: I 244 ILE cc_start: 0.7076 (pt) cc_final: 0.6798 (mt) REVERT: u 122 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5835 (ttp-170) REVERT: j 14 LYS cc_start: 0.6765 (mmtm) cc_final: 0.6311 (mppt) REVERT: x 500 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5423 (t80) outliers start: 37 outliers final: 18 residues processed: 304 average time/residue: 0.5954 time to fit residues: 289.9936 Evaluate side-chains 292 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 325 optimal weight: 0.7980 chunk 263 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 ASN j 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 45450 Z= 0.117 Angle : 0.440 8.579 64856 Z= 0.230 Chirality : 0.034 0.210 7899 Planarity : 0.003 0.045 5385 Dihedral : 20.954 179.227 15355 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.11 % Allowed : 10.16 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.15), residues: 3220 helix: 2.32 (0.14), residues: 1370 sheet: 0.52 (0.22), residues: 594 loop : -0.26 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.022 0.001 TYR p 238 ARG 0.011 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 4.147 Fit side-chains revert: symmetry clash REVERT: I 244 ILE cc_start: 0.7080 (pt) cc_final: 0.6806 (mt) REVERT: u 122 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5833 (ttp-170) REVERT: x 500 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5399 (t80) outliers start: 33 outliers final: 25 residues processed: 302 average time/residue: 0.6056 time to fit residues: 293.1810 Evaluate side-chains 300 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 273 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 317 optimal weight: 0.0970 chunk 176 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 200 optimal weight: 0.0370 overall best weight: 2.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 40 HIS ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 45450 Z= 0.255 Angle : 0.530 8.149 64856 Z= 0.275 Chirality : 0.038 0.259 7899 Planarity : 0.004 0.048 5385 Dihedral : 20.969 178.601 15355 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.55 % Allowed : 11.20 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3220 helix: 2.12 (0.14), residues: 1369 sheet: 0.31 (0.22), residues: 580 loop : -0.34 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 464 HIS 0.008 0.001 HIS 8 18 PHE 0.025 0.002 PHE x 61 TYR 0.027 0.002 TYR p 238 ARG 0.011 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 278 time to evaluate : 3.698 Fit side-chains revert: symmetry clash REVERT: G 54 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7633 (mt-10) REVERT: p 417 GLU cc_start: 0.6706 (pp20) cc_final: 0.6359 (pp20) REVERT: w 181 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: x 500 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5484 (t80) outliers start: 46 outliers final: 33 residues processed: 304 average time/residue: 0.6350 time to fit residues: 309.0051 Evaluate side-chains 309 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 181 GLU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 380 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 ASN c 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 45450 Z= 0.211 Angle : 0.502 8.387 64856 Z= 0.262 Chirality : 0.037 0.258 7899 Planarity : 0.004 0.050 5385 Dihedral : 20.972 178.911 15355 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.51 % Allowed : 11.60 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3220 helix: 2.12 (0.14), residues: 1370 sheet: 0.33 (0.22), residues: 591 loop : -0.40 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 464 HIS 0.007 0.001 HIS 8 18 PHE 0.023 0.002 PHE x 61 TYR 0.024 0.001 TYR p 96 ARG 0.012 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 277 time to evaluate : 3.721 Fit side-chains revert: symmetry clash REVERT: I 244 ILE cc_start: 0.7212 (pt) cc_final: 0.6868 (mt) REVERT: U 49 ASN cc_start: 0.7229 (t160) cc_final: 0.7000 (t0) REVERT: p 417 GLU cc_start: 0.6886 (pp20) cc_final: 0.6537 (pp20) REVERT: w 181 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6983 (pt0) REVERT: x 500 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5489 (t80) outliers start: 45 outliers final: 39 residues processed: 302 average time/residue: 0.6198 time to fit residues: 295.8495 Evaluate side-chains 313 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 272 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 181 GLU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 186 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 259 optimal weight: 0.0030 chunk 188 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: w 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 45450 Z= 0.107 Angle : 0.461 8.730 64856 Z= 0.243 Chirality : 0.034 0.233 7899 Planarity : 0.003 0.066 5385 Dihedral : 20.984 179.762 15355 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.28 % Allowed : 12.28 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.15), residues: 3220 helix: 2.26 (0.14), residues: 1370 sheet: 0.42 (0.22), residues: 589 loop : -0.32 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 464 HIS 0.003 0.001 HIS R 118 PHE 0.022 0.001 PHE x 61 TYR 0.029 0.001 TYR p 96 ARG 0.013 0.000 ARG u 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 273 time to evaluate : 3.624 Fit side-chains revert: symmetry clash REVERT: 5 77 ARG cc_start: 0.6351 (ttm170) cc_final: 0.5901 (mtm-85) REVERT: I 244 ILE cc_start: 0.7101 (pt) cc_final: 0.6818 (mt) REVERT: U 49 ASN cc_start: 0.7145 (t160) cc_final: 0.6941 (t0) REVERT: b 521 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8201 (mtt90) REVERT: p 417 GLU cc_start: 0.6798 (pp20) cc_final: 0.6508 (pp20) REVERT: w 181 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: x 500 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.5469 (t80) outliers start: 38 outliers final: 27 residues processed: 295 average time/residue: 0.6274 time to fit residues: 293.5740 Evaluate side-chains 297 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 181 GLU Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.8980 chunk 364 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 335 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 18 ASN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 45450 Z= 0.248 Angle : 0.519 8.094 64856 Z= 0.271 Chirality : 0.038 0.267 7899 Planarity : 0.004 0.047 5385 Dihedral : 20.961 178.923 15355 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 12.34 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3220 helix: 2.12 (0.14), residues: 1368 sheet: 0.33 (0.22), residues: 591 loop : -0.40 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 464 HIS 0.007 0.001 HIS 8 18 PHE 0.025 0.002 PHE x 61 TYR 0.025 0.002 TYR p 238 ARG 0.006 0.000 ARG u 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 3.790 Fit side-chains revert: symmetry clash REVERT: 5 77 ARG cc_start: 0.6111 (ttm170) cc_final: 0.5850 (mtm-85) REVERT: U 24 GLU cc_start: 0.6890 (mp0) cc_final: 0.6638 (mp0) REVERT: b 521 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8222 (mtt90) REVERT: w 181 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: x 500 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.5456 (t80) outliers start: 44 outliers final: 39 residues processed: 299 average time/residue: 0.6088 time to fit residues: 290.0011 Evaluate side-chains 311 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain p residue 408 THR Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 181 GLU Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 728 MET Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 186 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 2.9990 chunk 375 optimal weight: 0.4980 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 313 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 18 ASN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45450 Z= 0.181 Angle : 0.494 8.032 64856 Z= 0.259 Chirality : 0.036 0.257 7899 Planarity : 0.004 0.079 5385 Dihedral : 20.969 179.164 15355 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.35 % Allowed : 12.65 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3220 helix: 2.16 (0.14), residues: 1368 sheet: 0.34 (0.22), residues: 591 loop : -0.40 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 464 HIS 0.006 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.038 0.001 TYR p 96 ARG 0.015 0.000 ARG u 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 3.848 Fit side-chains revert: symmetry clash REVERT: 5 77 ARG cc_start: 0.6100 (ttm170) cc_final: 0.5856 (mtm-85) REVERT: U 24 GLU cc_start: 0.6938 (mp0) cc_final: 0.6689 (mp0) REVERT: w 181 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6968 (pt0) REVERT: x 500 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.5481 (t80) outliers start: 40 outliers final: 33 residues processed: 296 average time/residue: 0.6327 time to fit residues: 296.7066 Evaluate side-chains 305 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 270 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 271 ASP Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain p residue 408 THR Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 181 GLU Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 728 MET Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 322 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 ASN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129565 restraints weight = 55983.294| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.27 r_work: 0.3196 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 45450 Z= 0.247 Angle : 0.528 7.816 64856 Z= 0.276 Chirality : 0.038 0.275 7899 Planarity : 0.004 0.059 5385 Dihedral : 20.977 178.544 15355 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.45 % Allowed : 12.58 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3220 helix: 2.05 (0.14), residues: 1368 sheet: 0.27 (0.22), residues: 588 loop : -0.46 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 464 HIS 0.007 0.001 HIS 8 18 PHE 0.025 0.002 PHE x 61 TYR 0.027 0.002 TYR p 96 ARG 0.013 0.000 ARG u 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8141.25 seconds wall clock time: 150 minutes 16.72 seconds (9016.72 seconds total)