Starting phenix.real_space_refine on Fri Feb 16 01:25:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/02_2024/7tfl_25876_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 209 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 P 38 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 8526 2.51 5 N 2397 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 544": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13690 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2659 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 2 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2581 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2684 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "I" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.24, per 1000 atoms: 0.53 Number of scatterers: 13690 At special positions: 0 Unit cell: (86.94, 119.232, 128.34, 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) S 68 16.00 P 38 15.00 Mg 4 11.99 O 2657 8.00 N 2397 7.00 C 8526 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: 5.54 Conformation dependent library (CDL) restraints added in 2.1 seconds 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 7 sheets defined 55.1% alpha, 6.1% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 426 through 429 removed outlier: 3.617A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 527 removed outlier: 4.000A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.891A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 4.331A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 571' Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.805A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.586A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 610 through 631 removed outlier: 3.518A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 Proline residue: A 642 - end of helix removed outlier: 3.823A pdb=" N LEU A 647 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 669 through 677 removed outlier: 3.604A pdb=" N SER A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.648A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.513A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 78 removed outlier: 4.126A pdb=" N SER C 76 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 78 " --> pdb=" O TYR C 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 73 through 78' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.102A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.654A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.146A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 44 through 54 removed outlier: 4.028A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.015A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 removed outlier: 3.613A pdb=" N LEU D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.304A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.902A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 333 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.024A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.858A pdb=" N SER E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 296 through 309 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 Processing sheet with id= A, first strand: chain 'A' and resid 472 through 474 removed outlier: 5.867A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.567A pdb=" N ALA B 159 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER B 48 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 161 " --> pdb=" O SER B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 75 through 78 removed outlier: 7.240A pdb=" N ILE B 110 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 78 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 112 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 143 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 162 through 166 removed outlier: 4.264A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 80 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.647A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 61 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 168 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.269A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 68 through 76 removed outlier: 3.910A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4521 1.36 - 1.51: 3565 1.51 - 1.66: 5768 1.66 - 1.80: 61 1.80 - 1.95: 44 Bond restraints: 13959 Sorted by residual: bond pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N LEU A 549 " pdb=" CA LEU A 549 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N ALA A 548 " pdb=" CA ALA A 548 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.70e+00 bond pdb=" N LYS A 550 " pdb=" CA LYS A 550 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.22e+00 ... (remaining 13954 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.97: 530 106.97 - 114.23: 8357 114.23 - 121.49: 6915 121.49 - 128.75: 3090 128.75 - 136.01: 102 Bond angle restraints: 18994 Sorted by residual: angle pdb=" CA PRO C 239 " pdb=" N PRO C 239 " pdb=" CD PRO C 239 " ideal model delta sigma weight residual 112.00 105.95 6.05 1.40e+00 5.10e-01 1.87e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.12 116.46 -6.34 1.47e+00 4.63e-01 1.86e+01 angle pdb=" C ILE B 151 " pdb=" N GLU B 152 " pdb=" CA GLU B 152 " ideal model delta sigma weight residual 120.09 125.11 -5.02 1.25e+00 6.40e-01 1.62e+01 angle pdb=" CA ILE A 547 " pdb=" C ILE A 547 " pdb=" O ILE A 547 " ideal model delta sigma weight residual 121.63 118.04 3.59 9.90e-01 1.02e+00 1.31e+01 angle pdb=" CB LYS D 111 " pdb=" CG LYS D 111 " pdb=" CD LYS D 111 " ideal model delta sigma weight residual 111.30 119.46 -8.16 2.30e+00 1.89e-01 1.26e+01 ... (remaining 18989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 8109 28.10 - 56.19: 403 56.19 - 84.29: 31 84.29 - 112.38: 1 112.38 - 140.48: 2 Dihedral angle restraints: 8546 sinusoidal: 3715 harmonic: 4831 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -172.56 112.56 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" O1A AGS D 500 " pdb=" O3A AGS D 500 " pdb=" PA AGS D 500 " pdb=" PB AGS D 500 " ideal model delta sinusoidal sigma weight residual -67.73 72.75 -140.48 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA PHE A 346 " pdb=" C PHE A 346 " pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1616 0.041 - 0.082: 464 0.082 - 0.123: 112 0.123 - 0.165: 12 0.165 - 0.206: 3 Chirality restraints: 2207 Sorted by residual: chirality pdb=" CG LEU B 313 " pdb=" CB LEU B 313 " pdb=" CD1 LEU B 313 " pdb=" CD2 LEU B 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA LEU A 549 " pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CB LEU A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2204 not shown) Planarity restraints: 2316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 324 " -0.035 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP D 324 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 324 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 324 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 324 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 324 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 324 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 324 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 324 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 324 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 238 " -0.055 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 239 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 449 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 450 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.031 5.00e-02 4.00e+02 ... (remaining 2313 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 246 2.65 - 3.21: 13013 3.21 - 3.78: 22807 3.78 - 4.34: 29867 4.34 - 4.90: 47615 Nonbonded interactions: 113548 Sorted by model distance: nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.089 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.108 2.170 nonbonded pdb=" O3G AGS D 500 " pdb="MG MG E 401 " model vdw 2.111 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.123 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.187 2.170 ... (remaining 113543 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 13.860 Check model and map are aligned: 0.200 Set scattering table: 0.100 Process input model: 40.020 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 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 : 0.003 0.110 13959 Z= 0.168 Angle : 0.621 10.456 18994 Z= 0.316 Chirality : 0.041 0.206 2207 Planarity : 0.005 0.080 2316 Dihedral : 15.097 140.476 5404 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.21), residues: 1637 helix: 0.92 (0.17), residues: 927 sheet: 0.00 (0.48), residues: 132 loop : -0.22 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP D 324 HIS 0.005 0.001 HIS D 340 PHE 0.018 0.001 PHE A 346 TYR 0.014 0.001 TYR E 92 ARG 0.007 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LYS cc_start: 0.7309 (pptt) cc_final: 0.6821 (mmtt) REVERT: E 101 MET cc_start: 0.3852 (ppp) cc_final: 0.2888 (ppp) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.2319 time to fit residues: 83.8402 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 98 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13959 Z= 0.218 Angle : 0.579 8.758 18994 Z= 0.293 Chirality : 0.040 0.173 2207 Planarity : 0.004 0.037 2316 Dihedral : 12.850 151.130 2136 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.16 % Allowed : 10.00 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.21), residues: 1637 helix: 0.86 (0.17), residues: 961 sheet: -0.15 (0.49), residues: 122 loop : -0.33 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 324 HIS 0.008 0.001 HIS B 108 PHE 0.024 0.002 PHE A 443 TYR 0.017 0.001 TYR D 129 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 PHE cc_start: 0.3196 (m-10) cc_final: 0.2303 (m-80) REVERT: E 101 MET cc_start: 0.4187 (ppp) cc_final: 0.2998 (ppp) outliers start: 17 outliers final: 9 residues processed: 213 average time/residue: 0.2366 time to fit residues: 76.3814 Evaluate side-chains 194 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 124 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 12 ASN C 105 GLN E 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13959 Z= 0.148 Angle : 0.529 7.874 18994 Z= 0.267 Chirality : 0.038 0.173 2207 Planarity : 0.004 0.036 2316 Dihedral : 12.730 148.030 2136 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.23 % Allowed : 12.05 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.22), residues: 1637 helix: 1.10 (0.17), residues: 961 sheet: -0.46 (0.48), residues: 128 loop : -0.22 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.009 0.001 HIS C 298 PHE 0.020 0.001 PHE D 290 TYR 0.015 0.001 TYR D 129 ARG 0.003 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6749 (mt-10) REVERT: C 166 PHE cc_start: 0.3143 (m-10) cc_final: 0.2459 (m-10) REVERT: E 101 MET cc_start: 0.4152 (ppp) cc_final: 0.2956 (ppp) outliers start: 18 outliers final: 12 residues processed: 212 average time/residue: 0.2366 time to fit residues: 76.2411 Evaluate side-chains 197 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13959 Z= 0.154 Angle : 0.528 9.733 18994 Z= 0.265 Chirality : 0.038 0.145 2207 Planarity : 0.004 0.035 2316 Dihedral : 12.750 152.198 2136 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.99 % Allowed : 12.81 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.22), residues: 1637 helix: 1.23 (0.17), residues: 962 sheet: -0.59 (0.47), residues: 134 loop : -0.15 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.007 0.001 HIS C 298 PHE 0.027 0.001 PHE D 203 TYR 0.017 0.001 TYR D 129 ARG 0.004 0.000 ARG E 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.3784 (mmp) cc_final: 0.2288 (mtt) REVERT: C 166 PHE cc_start: 0.3380 (m-10) cc_final: 0.2734 (m-10) REVERT: D 350 ILE cc_start: 0.7705 (pt) cc_final: 0.7469 (mt) REVERT: E 101 MET cc_start: 0.4259 (ppp) cc_final: 0.3009 (ppp) outliers start: 29 outliers final: 19 residues processed: 211 average time/residue: 0.2352 time to fit residues: 76.1173 Evaluate side-chains 205 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 333 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13959 Z= 0.244 Angle : 0.601 8.975 18994 Z= 0.300 Chirality : 0.041 0.199 2207 Planarity : 0.004 0.038 2316 Dihedral : 13.098 164.335 2136 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.26 % Allowed : 13.97 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.22), residues: 1637 helix: 1.03 (0.17), residues: 966 sheet: -1.18 (0.45), residues: 131 loop : -0.19 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 327 HIS 0.006 0.001 HIS C 298 PHE 0.025 0.002 PHE D 203 TYR 0.016 0.001 TYR D 129 ARG 0.004 0.000 ARG E 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4120 (mmp) cc_final: 0.2719 (mtt) REVERT: B 83 ASP cc_start: 0.5036 (m-30) cc_final: 0.3708 (p0) REVERT: D 145 MET cc_start: 0.6193 (ptt) cc_final: 0.5870 (ptm) REVERT: E 101 MET cc_start: 0.4265 (ppp) cc_final: 0.3162 (ppp) REVERT: E 287 TYR cc_start: 0.7317 (m-80) cc_final: 0.6950 (m-80) outliers start: 33 outliers final: 25 residues processed: 229 average time/residue: 0.2441 time to fit residues: 83.1574 Evaluate side-chains 214 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 210 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13959 Z= 0.361 Angle : 0.741 9.619 18994 Z= 0.371 Chirality : 0.045 0.185 2207 Planarity : 0.005 0.056 2316 Dihedral : 13.789 174.273 2136 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.29 % Allowed : 16.03 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.21), residues: 1637 helix: 0.38 (0.17), residues: 970 sheet: -1.34 (0.47), residues: 129 loop : -0.70 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 298 HIS 0.008 0.002 HIS B 296 PHE 0.039 0.003 PHE D 203 TYR 0.018 0.002 TYR B 71 ARG 0.009 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 ILE cc_start: 0.5156 (OUTLIER) cc_final: 0.4906 (mp) REVERT: A 463 MET cc_start: 0.4195 (mmp) cc_final: 0.3314 (mtt) REVERT: A 594 GLU cc_start: 0.6725 (tp30) cc_final: 0.5745 (tp30) REVERT: B 45 MET cc_start: 0.4740 (mtt) cc_final: 0.4525 (mtt) REVERT: B 83 ASP cc_start: 0.5165 (m-30) cc_final: 0.3850 (p0) REVERT: B 119 MET cc_start: 0.6261 (mtt) cc_final: 0.5806 (mtm) REVERT: B 290 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6746 (ptmt) REVERT: C 22 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6995 (mt-10) REVERT: E 101 MET cc_start: 0.4492 (ppp) cc_final: 0.3310 (ppp) outliers start: 48 outliers final: 32 residues processed: 236 average time/residue: 0.2534 time to fit residues: 88.2371 Evaluate side-chains 211 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13959 Z= 0.192 Angle : 0.626 11.788 18994 Z= 0.312 Chirality : 0.041 0.384 2207 Planarity : 0.004 0.049 2316 Dihedral : 13.518 164.613 2136 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.33 % Allowed : 18.22 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.21), residues: 1637 helix: 0.73 (0.17), residues: 971 sheet: -1.15 (0.47), residues: 129 loop : -0.43 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 324 HIS 0.006 0.001 HIS A 610 PHE 0.025 0.002 PHE A 346 TYR 0.015 0.002 TYR D 129 ARG 0.005 0.000 ARG E 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLU cc_start: 0.6473 (tp30) cc_final: 0.5766 (tp30) REVERT: B 83 ASP cc_start: 0.5005 (m-30) cc_final: 0.3759 (p0) REVERT: B 119 MET cc_start: 0.6078 (mtt) cc_final: 0.5858 (mtm) REVERT: C 22 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7020 (mt-10) REVERT: E 101 MET cc_start: 0.4472 (ppp) cc_final: 0.3399 (ppp) outliers start: 34 outliers final: 27 residues processed: 215 average time/residue: 0.2417 time to fit residues: 78.3922 Evaluate side-chains 211 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13959 Z= 0.211 Angle : 0.636 12.083 18994 Z= 0.314 Chirality : 0.042 0.403 2207 Planarity : 0.004 0.057 2316 Dihedral : 13.582 165.086 2136 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 18.49 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.22), residues: 1637 helix: 0.75 (0.17), residues: 980 sheet: -1.19 (0.47), residues: 129 loop : -0.31 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 324 HIS 0.008 0.001 HIS C 298 PHE 0.023 0.002 PHE A 346 TYR 0.014 0.001 TYR D 129 ARG 0.008 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.6235 (p90) cc_final: 0.6002 (p90) REVERT: A 421 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4832 (mp) REVERT: A 463 MET cc_start: 0.3910 (mmp) cc_final: 0.2814 (mtt) REVERT: B 83 ASP cc_start: 0.5004 (m-30) cc_final: 0.3802 (p0) REVERT: C 22 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7008 (mt-10) REVERT: E 101 MET cc_start: 0.4533 (ppp) cc_final: 0.3482 (ppp) REVERT: E 287 TYR cc_start: 0.7501 (m-80) cc_final: 0.6830 (m-80) outliers start: 36 outliers final: 31 residues processed: 218 average time/residue: 0.2357 time to fit residues: 77.8048 Evaluate side-chains 219 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 330 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.0060 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13959 Z= 0.204 Angle : 0.636 12.288 18994 Z= 0.315 Chirality : 0.042 0.397 2207 Planarity : 0.004 0.046 2316 Dihedral : 13.564 162.584 2136 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.47 % Allowed : 19.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.22), residues: 1637 helix: 0.77 (0.17), residues: 978 sheet: -1.22 (0.46), residues: 129 loop : -0.27 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 324 HIS 0.005 0.001 HIS A 610 PHE 0.023 0.002 PHE A 346 TYR 0.017 0.001 TYR A 651 ARG 0.007 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.6263 (p90) cc_final: 0.6028 (p90) REVERT: A 421 ILE cc_start: 0.5074 (OUTLIER) cc_final: 0.4826 (mp) REVERT: A 463 MET cc_start: 0.3959 (mmp) cc_final: 0.2978 (mtt) REVERT: A 655 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7233 (mttt) REVERT: B 83 ASP cc_start: 0.5080 (m-30) cc_final: 0.3843 (p0) REVERT: C 22 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7006 (mt-10) REVERT: D 111 LYS cc_start: 0.6666 (mmmt) cc_final: 0.6368 (tppt) REVERT: E 101 MET cc_start: 0.4535 (ppp) cc_final: 0.3495 (ppp) REVERT: E 287 TYR cc_start: 0.7551 (m-80) cc_final: 0.6903 (m-80) outliers start: 36 outliers final: 31 residues processed: 214 average time/residue: 0.2391 time to fit residues: 76.5885 Evaluate side-chains 216 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13959 Z= 0.193 Angle : 0.645 12.391 18994 Z= 0.317 Chirality : 0.043 0.390 2207 Planarity : 0.004 0.043 2316 Dihedral : 13.518 160.339 2136 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.40 % Allowed : 19.11 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.22), residues: 1637 helix: 0.79 (0.17), residues: 976 sheet: -1.23 (0.46), residues: 129 loop : -0.17 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 324 HIS 0.005 0.001 HIS A 610 PHE 0.024 0.002 PHE A 346 TYR 0.015 0.001 TYR D 129 ARG 0.006 0.000 ARG C 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.6233 (p90) cc_final: 0.5994 (p90) REVERT: A 421 ILE cc_start: 0.5062 (OUTLIER) cc_final: 0.4807 (mp) REVERT: A 463 MET cc_start: 0.3935 (mmp) cc_final: 0.3063 (mtt) REVERT: A 594 GLU cc_start: 0.6539 (tp30) cc_final: 0.5568 (tp30) REVERT: B 83 ASP cc_start: 0.5046 (m-30) cc_final: 0.3846 (p0) REVERT: C 22 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7033 (mt-10) REVERT: C 232 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7562 (mm) REVERT: D 111 LYS cc_start: 0.6557 (mmmt) cc_final: 0.6296 (tppt) REVERT: D 259 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7337 (mm) REVERT: E 101 MET cc_start: 0.4483 (ppp) cc_final: 0.3446 (ppp) outliers start: 35 outliers final: 30 residues processed: 216 average time/residue: 0.2355 time to fit residues: 76.9294 Evaluate side-chains 221 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 115 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.171685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.150377 restraints weight = 25430.717| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.93 r_work: 0.4199 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13959 Z= 0.196 Angle : 0.646 12.240 18994 Z= 0.317 Chirality : 0.043 0.426 2207 Planarity : 0.004 0.042 2316 Dihedral : 13.525 160.735 2136 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.74 % Allowed : 18.90 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.22), residues: 1637 helix: 0.82 (0.17), residues: 975 sheet: -1.24 (0.46), residues: 129 loop : -0.14 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 324 HIS 0.005 0.001 HIS A 610 PHE 0.023 0.001 PHE A 346 TYR 0.018 0.001 TYR E 287 ARG 0.006 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.20 seconds wall clock time: 58 minutes 40.60 seconds (3520.60 seconds total)