Starting phenix.real_space_refine on Tue Sep 24 22:29:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/09_2024/6j5w_0683.cif" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 57 5.16 5 C 5677 2.51 5 N 1548 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2455 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 6503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6503 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 788} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.60 Number of scatterers: 8985 At special positions: 0 Unit cell: (87.28, 93.826, 123.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 2 15.00 O 1701 8.00 N 1548 7.00 C 5677 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 43.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 16 through 39 removed outlier: 3.564A pdb=" N LYS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.757A pdb=" N ILE B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 114 removed outlier: 4.180A pdb=" N GLU B 103 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 161 through 182 removed outlier: 3.733A pdb=" N ILE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 247 through 264 removed outlier: 3.912A pdb=" N VAL B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 289 removed outlier: 3.624A pdb=" N LEU B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.603A pdb=" N LEU B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.542A pdb=" N VAL B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 removed outlier: 4.027A pdb=" N VAL A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 42 removed outlier: 4.414A pdb=" N LYS A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.628A pdb=" N GLU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.121A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.729A pdb=" N SER A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.814A pdb=" N LYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 4.334A pdb=" N ILE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.813A pdb=" N SER A 180 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 200 removed outlier: 3.938A pdb=" N ILE A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.737A pdb=" N LYS A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.574A pdb=" N LYS A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.752A pdb=" N VAL A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.914A pdb=" N CYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.703A pdb=" N ILE A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.765A pdb=" N VAL A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.736A pdb=" N LYS A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 removed outlier: 3.570A pdb=" N TYR A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 425' Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.703A pdb=" N GLY A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.912A pdb=" N CYS A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.566A pdb=" N ARG A 492 " --> pdb=" O HIS A 488 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.961A pdb=" N GLU A 607 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.852A pdb=" N ILE A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 631 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 4.472A pdb=" N GLY A 655 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 657 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 683 removed outlier: 3.796A pdb=" N LYS A 681 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A 682 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.666A pdb=" N ILE A 699 " --> pdb=" O GLY A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.685A pdb=" N LEU A 704 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.996A pdb=" N ILE A 708 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN A 709 " --> pdb=" O SER A 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 705 through 709' Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 780 through 785 removed outlier: 4.102A pdb=" N TRP A 784 " --> pdb=" O GLN A 780 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 785' Processing helix chain 'A' and resid 808 through 815 Processing sheet with id=AA1, first strand: chain 'B' and resid 72 through 79 removed outlier: 3.566A pdb=" N ARG B 82 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 127 removed outlier: 4.177A pdb=" N GLY B 125 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.469A pdb=" N ILE A 216 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP A 267 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 218 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 264 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 295 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N MET A 266 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS A 313 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 186 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA6, first strand: chain 'A' and resid 515 through 517 removed outlier: 3.536A pdb=" N VAL A 536 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 591 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 640 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 746 removed outlier: 3.583A pdb=" N SER A 770 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A 796 " --> pdb=" O THR A 822 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.66 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: 2633 1.33 - 1.46: 1752 1.46 - 1.58: 4683 1.58 - 1.70: 3 1.70 - 1.82: 83 Bond restraints: 9154 Sorted by residual: bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.453 0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" CB CYS B 257 " pdb=" SG CYS B 257 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta sigma weight residual 1.528 1.556 -0.027 1.67e-02 3.59e+03 2.66e+00 bond pdb=" CG1 ILE A 614 " pdb=" CD1 ILE A 614 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.49e+00 bond pdb=" C ALA B 182 " pdb=" N PHE B 183 " ideal model delta sigma weight residual 1.329 1.282 0.047 3.03e-02 1.09e+03 2.40e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 12119 3.46 - 6.93: 205 6.93 - 10.39: 37 10.39 - 13.85: 5 13.85 - 17.31: 2 Bond angle restraints: 12368 Sorted by residual: angle pdb=" C GLU B 80 " pdb=" N ASP B 81 " pdb=" CA ASP B 81 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C SER B 208 " pdb=" N ASP B 209 " pdb=" CA ASP B 209 " ideal model delta sigma weight residual 121.54 131.84 -10.30 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C ILE B 152 " pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta sigma weight residual 121.97 131.52 -9.55 1.80e+00 3.09e-01 2.81e+01 angle pdb=" N VAL B 153 " pdb=" CA VAL B 153 " pdb=" C VAL B 153 " ideal model delta sigma weight residual 109.34 98.98 10.36 2.08e+00 2.31e-01 2.48e+01 angle pdb=" CA LEU A 623 " pdb=" CB LEU A 623 " pdb=" CG LEU A 623 " ideal model delta sigma weight residual 116.30 133.61 -17.31 3.50e+00 8.16e-02 2.45e+01 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 5044 15.03 - 30.05: 407 30.05 - 45.08: 98 45.08 - 60.11: 10 60.11 - 75.14: 3 Dihedral angle restraints: 5562 sinusoidal: 2307 harmonic: 3255 Sorted by residual: dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta harmonic sigma weight residual 180.00 127.50 52.50 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA CYS A 649 " pdb=" C CYS A 649 " pdb=" N PHE A 650 " pdb=" CA PHE A 650 " ideal model delta harmonic sigma weight residual 180.00 129.38 50.62 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA GLU B 156 " pdb=" C GLU B 156 " pdb=" N GLU B 157 " pdb=" CA GLU B 157 " ideal model delta harmonic sigma weight residual 180.00 130.41 49.59 0 5.00e+00 4.00e-02 9.84e+01 ... (remaining 5559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 922 0.061 - 0.122: 390 0.122 - 0.183: 60 0.183 - 0.244: 15 0.244 - 0.305: 4 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE A 582 " pdb=" CA ILE A 582 " pdb=" CG1 ILE A 582 " pdb=" CG2 ILE A 582 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A 494 " pdb=" CB LEU A 494 " pdb=" CD1 LEU A 494 " pdb=" CD2 LEU A 494 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1388 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 649 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C CYS A 649 " -0.059 2.00e-02 2.50e+03 pdb=" O CYS A 649 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A 650 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 80 " -0.013 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C GLU B 80 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU B 80 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP B 81 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO B 44 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.034 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1733 2.77 - 3.30: 8320 3.30 - 3.83: 14108 3.83 - 4.37: 16463 4.37 - 4.90: 27777 Nonbonded interactions: 68401 Sorted by model distance: nonbonded pdb=" O VAL B 151 " pdb=" OG SER B 158 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A 267 " pdb=" OG1 THR A 295 " model vdw 2.278 3.040 nonbonded pdb=" O LEU B 123 " pdb=" OH TYR A 721 " model vdw 2.317 3.040 nonbonded pdb=" OG SER A 773 " pdb=" OG SER A 800 " model vdw 2.339 3.040 nonbonded pdb=" O ASN B 116 " pdb=" OG SER A 773 " model vdw 2.346 3.040 ... (remaining 68396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.370 Find NCS groups from input model: 0.230 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.008 0.062 9154 Z= 0.498 Angle : 1.206 17.313 12368 Z= 0.624 Chirality : 0.067 0.305 1391 Planarity : 0.007 0.062 1576 Dihedral : 11.811 75.137 3452 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.04 % Favored : 88.51 % Rotamer: Outliers : 0.89 % Allowed : 5.54 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.62 (0.20), residues: 1114 helix: -3.61 (0.15), residues: 427 sheet: -3.22 (0.39), residues: 113 loop : -2.53 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 96 HIS 0.012 0.002 HIS A 597 PHE 0.028 0.004 PHE B 120 TYR 0.037 0.003 TYR A 109 ARG 0.012 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8392 (t0) cc_final: 0.8187 (t0) REVERT: B 171 GLU cc_start: 0.8479 (tp30) cc_final: 0.8264 (tp30) REVERT: B 247 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 335 GLN cc_start: 0.8658 (tt0) cc_final: 0.8068 (tt0) REVERT: B 342 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7734 (tp-100) REVERT: A 20 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (ttpt) REVERT: A 29 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8486 (mmtm) REVERT: A 169 LYS cc_start: 0.8449 (mptt) cc_final: 0.8000 (mmtm) REVERT: A 277 TRP cc_start: 0.5944 (t60) cc_final: 0.5649 (t60) REVERT: A 498 ILE cc_start: 0.9302 (tp) cc_final: 0.9030 (tp) REVERT: A 506 ASN cc_start: 0.7681 (t0) cc_final: 0.6718 (p0) REVERT: A 548 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8784 (t0) REVERT: A 572 ASP cc_start: 0.8039 (t0) cc_final: 0.7685 (t0) REVERT: A 612 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9042 (tt) REVERT: A 828 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7716 (mp0) outliers start: 9 outliers final: 1 residues processed: 210 average time/residue: 0.2586 time to fit residues: 72.2390 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.0020 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN B 119 ASN B 174 ASN B 180 HIS A 42 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 548 ASN A 643 ASN A 742 HIS A 761 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9154 Z= 0.165 Angle : 0.733 11.945 12368 Z= 0.369 Chirality : 0.046 0.194 1391 Planarity : 0.005 0.046 1576 Dihedral : 7.624 50.389 1227 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.80 % Favored : 91.02 % Rotamer: Outliers : 3.07 % Allowed : 10.09 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.67 (0.23), residues: 1114 helix: -2.55 (0.19), residues: 449 sheet: -2.72 (0.42), residues: 113 loop : -2.18 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 825 HIS 0.010 0.001 HIS A 597 PHE 0.014 0.001 PHE A 748 TYR 0.027 0.001 TYR A 27 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.8213 (tt0) cc_final: 0.7870 (tp30) REVERT: B 37 ASP cc_start: 0.8485 (t0) cc_final: 0.8157 (t0) REVERT: B 102 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7698 (pttm) REVERT: B 339 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: A 29 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8178 (mmtm) REVERT: A 169 LYS cc_start: 0.8276 (mptt) cc_final: 0.7761 (mtmt) REVERT: A 277 TRP cc_start: 0.5982 (t60) cc_final: 0.5736 (t60) REVERT: A 391 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: A 498 ILE cc_start: 0.9194 (tp) cc_final: 0.8897 (tp) REVERT: A 612 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8886 (tt) REVERT: A 622 ASN cc_start: 0.8307 (p0) cc_final: 0.7566 (p0) REVERT: A 828 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7855 (mp0) outliers start: 31 outliers final: 11 residues processed: 184 average time/residue: 0.2380 time to fit residues: 59.4685 Evaluate side-chains 137 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 804 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 chunk 99 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS A 42 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 414 HIS A 450 ASN ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9154 Z= 0.159 Angle : 0.702 11.335 12368 Z= 0.347 Chirality : 0.046 0.215 1391 Planarity : 0.004 0.042 1576 Dihedral : 6.856 50.123 1221 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.53 % Favored : 91.29 % Rotamer: Outliers : 3.56 % Allowed : 11.67 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.24), residues: 1114 helix: -1.85 (0.22), residues: 449 sheet: -2.54 (0.41), residues: 130 loop : -1.82 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.008 0.001 HIS A 597 PHE 0.034 0.002 PHE B 139 TYR 0.020 0.001 TYR A 27 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.8179 (tt0) cc_final: 0.7888 (tp30) REVERT: B 37 ASP cc_start: 0.8468 (t0) cc_final: 0.8007 (t0) REVERT: B 185 LYS cc_start: 0.8650 (pttp) cc_final: 0.8402 (pttp) REVERT: B 269 MET cc_start: 0.6234 (ttt) cc_final: 0.5928 (tmm) REVERT: B 333 MET cc_start: 0.8513 (mmm) cc_final: 0.8235 (tpp) REVERT: B 339 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: A 29 LYS cc_start: 0.8790 (tmmt) cc_final: 0.8291 (mmtm) REVERT: A 64 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 169 LYS cc_start: 0.8309 (mptt) cc_final: 0.7762 (mtmt) REVERT: A 391 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6752 (ptp90) REVERT: A 427 GLU cc_start: 0.7782 (tt0) cc_final: 0.7578 (tt0) REVERT: A 498 ILE cc_start: 0.9220 (tp) cc_final: 0.8976 (tp) REVERT: A 622 ASN cc_start: 0.8202 (p0) cc_final: 0.7441 (p0) REVERT: A 634 LYS cc_start: 0.6912 (mppt) cc_final: 0.6628 (mmtt) REVERT: A 817 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.4857 (p90) REVERT: A 828 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7926 (mp0) outliers start: 36 outliers final: 21 residues processed: 169 average time/residue: 0.2134 time to fit residues: 49.8993 Evaluate side-chains 150 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 342 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9154 Z= 0.210 Angle : 0.702 11.238 12368 Z= 0.349 Chirality : 0.047 0.163 1391 Planarity : 0.004 0.041 1576 Dihedral : 6.738 52.601 1221 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.07 % Favored : 90.75 % Rotamer: Outliers : 3.76 % Allowed : 12.66 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.25), residues: 1114 helix: -1.43 (0.23), residues: 449 sheet: -2.29 (0.45), residues: 124 loop : -1.68 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 162 HIS 0.008 0.001 HIS A 597 PHE 0.016 0.002 PHE A 633 TYR 0.017 0.001 TYR A 27 ARG 0.004 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8483 (t0) cc_final: 0.8020 (t0) REVERT: B 106 ASN cc_start: 0.8938 (t0) cc_final: 0.8305 (t0) REVERT: B 185 LYS cc_start: 0.8656 (pttp) cc_final: 0.8414 (pttp) REVERT: B 269 MET cc_start: 0.6308 (ttt) cc_final: 0.5468 (ptm) REVERT: B 333 MET cc_start: 0.8505 (mmm) cc_final: 0.8130 (tpp) REVERT: B 339 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7646 (mm-30) REVERT: A 39 LYS cc_start: 0.7984 (mptt) cc_final: 0.7763 (mptt) REVERT: A 169 LYS cc_start: 0.8368 (mptt) cc_final: 0.7825 (mtmt) REVERT: A 391 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6519 (ptp90) REVERT: A 599 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6601 (pt) REVERT: A 606 MET cc_start: 0.9058 (ttp) cc_final: 0.8757 (ttm) REVERT: A 612 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8914 (tt) REVERT: A 622 ASN cc_start: 0.8114 (p0) cc_final: 0.7311 (p0) REVERT: A 649 CYS cc_start: 0.7527 (p) cc_final: 0.7308 (p) REVERT: A 817 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.5252 (p90) REVERT: A 828 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7963 (mp0) outliers start: 38 outliers final: 23 residues processed: 160 average time/residue: 0.1987 time to fit residues: 44.8644 Evaluate side-chains 144 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN A 204 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9154 Z= 0.157 Angle : 0.668 11.217 12368 Z= 0.330 Chirality : 0.045 0.157 1391 Planarity : 0.003 0.040 1576 Dihedral : 6.449 53.976 1221 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.96 % Allowed : 13.75 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.25), residues: 1114 helix: -1.06 (0.24), residues: 444 sheet: -2.15 (0.45), residues: 131 loop : -1.42 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 277 HIS 0.006 0.001 HIS A 597 PHE 0.024 0.001 PHE B 139 TYR 0.015 0.001 TYR A 27 ARG 0.005 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8552 (t0) cc_final: 0.8066 (t0) REVERT: B 68 GLN cc_start: 0.8235 (pp30) cc_final: 0.7949 (pp30) REVERT: B 106 ASN cc_start: 0.8757 (t0) cc_final: 0.8260 (t0) REVERT: B 269 MET cc_start: 0.6116 (ttt) cc_final: 0.5883 (ptm) REVERT: B 333 MET cc_start: 0.8371 (mmm) cc_final: 0.8153 (mmm) REVERT: B 339 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7598 (mm-30) REVERT: A 29 LYS cc_start: 0.9063 (tmmt) cc_final: 0.8546 (mmtm) REVERT: A 606 MET cc_start: 0.8932 (ttp) cc_final: 0.8691 (ttm) REVERT: A 649 CYS cc_start: 0.7500 (p) cc_final: 0.7245 (p) REVERT: A 741 LEU cc_start: 0.8227 (tt) cc_final: 0.7795 (tt) REVERT: A 817 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.5047 (p90) REVERT: A 828 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7842 (mp0) outliers start: 40 outliers final: 24 residues processed: 168 average time/residue: 0.1960 time to fit residues: 47.3135 Evaluate side-chains 147 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN A 42 GLN A 204 ASN A 210 HIS ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS A 622 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9154 Z= 0.303 Angle : 0.745 11.032 12368 Z= 0.371 Chirality : 0.048 0.175 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.763 55.317 1221 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.34 % Favored : 90.57 % Rotamer: Outliers : 4.45 % Allowed : 14.64 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.26), residues: 1114 helix: -1.07 (0.24), residues: 445 sheet: -2.04 (0.46), residues: 131 loop : -1.44 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 277 HIS 0.008 0.001 HIS A 597 PHE 0.022 0.002 PHE A 633 TYR 0.015 0.002 TYR A 27 ARG 0.005 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 0.962 Fit side-chains REVERT: B 33 GLU cc_start: 0.8169 (tt0) cc_final: 0.7938 (tp30) REVERT: B 37 ASP cc_start: 0.8594 (t0) cc_final: 0.8043 (t0) REVERT: B 68 GLN cc_start: 0.8453 (pp30) cc_final: 0.8066 (pp30) REVERT: B 106 ASN cc_start: 0.8781 (t0) cc_final: 0.8173 (t0) REVERT: B 269 MET cc_start: 0.6095 (ttt) cc_final: 0.5825 (ptm) REVERT: B 333 MET cc_start: 0.8451 (mmm) cc_final: 0.8207 (mmm) REVERT: B 339 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7605 (mm-30) REVERT: A 29 LYS cc_start: 0.9133 (tmmt) cc_final: 0.8877 (tmmt) REVERT: A 391 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6373 (ptp90) REVERT: A 599 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6991 (pt) REVERT: A 612 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 649 CYS cc_start: 0.7525 (p) cc_final: 0.7278 (p) REVERT: A 817 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.5472 (p90) REVERT: A 828 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8006 (mp0) outliers start: 45 outliers final: 27 residues processed: 151 average time/residue: 0.2035 time to fit residues: 43.5490 Evaluate side-chains 141 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9154 Z= 0.167 Angle : 0.704 15.298 12368 Z= 0.345 Chirality : 0.045 0.160 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.483 54.349 1221 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 4.06 % Allowed : 15.33 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.90 (0.26), residues: 1114 helix: -0.86 (0.24), residues: 445 sheet: -1.93 (0.46), residues: 131 loop : -1.32 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.006 0.001 HIS A 597 PHE 0.024 0.001 PHE B 139 TYR 0.014 0.001 TYR A 27 ARG 0.002 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 33 GLU cc_start: 0.8092 (tt0) cc_final: 0.7876 (tp30) REVERT: B 37 ASP cc_start: 0.8523 (t0) cc_final: 0.7991 (t0) REVERT: B 68 GLN cc_start: 0.8406 (pp30) cc_final: 0.8072 (pp30) REVERT: B 106 ASN cc_start: 0.8763 (t0) cc_final: 0.8179 (t0) REVERT: B 171 GLU cc_start: 0.8322 (tp30) cc_final: 0.8089 (tp30) REVERT: B 253 SER cc_start: 0.9332 (m) cc_final: 0.8565 (t) REVERT: B 269 MET cc_start: 0.6043 (ttt) cc_final: 0.5797 (ptm) REVERT: B 339 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7587 (mm-30) REVERT: A 29 LYS cc_start: 0.9076 (tmmt) cc_final: 0.8822 (tmmt) REVERT: A 391 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6224 (ptp90) REVERT: A 599 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6854 (pt) REVERT: A 649 CYS cc_start: 0.7570 (p) cc_final: 0.7336 (p) REVERT: A 817 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5175 (p90) REVERT: A 828 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8012 (mp0) outliers start: 41 outliers final: 27 residues processed: 153 average time/residue: 0.1964 time to fit residues: 43.1319 Evaluate side-chains 145 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.0050 chunk 102 optimal weight: 0.0970 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9154 Z= 0.152 Angle : 0.684 13.699 12368 Z= 0.334 Chirality : 0.045 0.154 1391 Planarity : 0.004 0.041 1576 Dihedral : 6.279 57.734 1221 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.74 % Rotamer: Outliers : 3.17 % Allowed : 15.92 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.65 (0.26), residues: 1114 helix: -0.62 (0.25), residues: 446 sheet: -1.76 (0.47), residues: 131 loop : -1.23 (0.30), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 277 HIS 0.007 0.001 HIS A 597 PHE 0.011 0.001 PHE A 748 TYR 0.012 0.001 TYR A 27 ARG 0.003 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.074 Fit side-chains REVERT: B 33 GLU cc_start: 0.8112 (tt0) cc_final: 0.7891 (tp30) REVERT: B 37 ASP cc_start: 0.8617 (t0) cc_final: 0.8068 (t0) REVERT: B 68 GLN cc_start: 0.8409 (pp30) cc_final: 0.8019 (pp30) REVERT: B 106 ASN cc_start: 0.8785 (t0) cc_final: 0.8185 (t0) REVERT: B 201 LYS cc_start: 0.9058 (pmtt) cc_final: 0.8661 (mmmt) REVERT: B 253 SER cc_start: 0.9323 (m) cc_final: 0.8554 (t) REVERT: B 339 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7526 (mm-30) REVERT: A 29 LYS cc_start: 0.8980 (tmmt) cc_final: 0.8733 (tmtt) REVERT: A 204 ASN cc_start: 0.8499 (m-40) cc_final: 0.8143 (t0) REVERT: A 586 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7407 (mm110) REVERT: A 599 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6589 (pt) REVERT: A 649 CYS cc_start: 0.7615 (p) cc_final: 0.7341 (p) REVERT: A 656 SER cc_start: 0.8812 (m) cc_final: 0.8512 (p) REVERT: A 741 LEU cc_start: 0.8343 (tt) cc_final: 0.7812 (tt) REVERT: A 817 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5051 (p90) REVERT: A 825 TRP cc_start: 0.8662 (m100) cc_final: 0.8304 (m100) REVERT: A 828 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7851 (mp0) outliers start: 32 outliers final: 22 residues processed: 160 average time/residue: 0.1952 time to fit residues: 44.4952 Evaluate side-chains 149 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9154 Z= 0.172 Angle : 0.700 12.904 12368 Z= 0.339 Chirality : 0.046 0.207 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.205 53.012 1221 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.26 % Favored : 91.65 % Rotamer: Outliers : 2.67 % Allowed : 17.11 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.64 (0.26), residues: 1114 helix: -0.66 (0.24), residues: 452 sheet: -1.63 (0.47), residues: 131 loop : -1.21 (0.30), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 277 HIS 0.013 0.001 HIS A 597 PHE 0.011 0.001 PHE A 748 TYR 0.013 0.001 TYR A 27 ARG 0.005 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.148 Fit side-chains REVERT: B 33 GLU cc_start: 0.8062 (tt0) cc_final: 0.7859 (tp30) REVERT: B 37 ASP cc_start: 0.8566 (t0) cc_final: 0.8035 (t0) REVERT: B 106 ASN cc_start: 0.8785 (t0) cc_final: 0.8172 (t0) REVERT: B 253 SER cc_start: 0.9345 (m) cc_final: 0.8585 (t) REVERT: B 339 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7563 (mm-30) REVERT: A 29 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8767 (tmmt) REVERT: A 104 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7865 (ppp80) REVERT: A 586 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7467 (mm110) REVERT: A 599 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6792 (pt) REVERT: A 649 CYS cc_start: 0.7573 (p) cc_final: 0.7291 (p) REVERT: A 656 SER cc_start: 0.8853 (m) cc_final: 0.8518 (p) REVERT: A 741 LEU cc_start: 0.8359 (tt) cc_final: 0.7867 (tt) REVERT: A 817 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5084 (p90) REVERT: A 825 TRP cc_start: 0.8689 (m100) cc_final: 0.8326 (m100) REVERT: A 828 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7864 (mp0) outliers start: 27 outliers final: 23 residues processed: 148 average time/residue: 0.1829 time to fit residues: 39.5036 Evaluate side-chains 148 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9154 Z= 0.187 Angle : 0.706 12.693 12368 Z= 0.344 Chirality : 0.046 0.194 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.122 53.834 1221 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 2.97 % Allowed : 16.72 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.63 (0.26), residues: 1114 helix: -0.67 (0.24), residues: 455 sheet: -1.54 (0.47), residues: 140 loop : -1.19 (0.30), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 277 HIS 0.013 0.001 HIS A 597 PHE 0.012 0.001 PHE A 633 TYR 0.016 0.001 TYR B 71 ARG 0.004 0.000 ARG A 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.137 Fit side-chains REVERT: B 37 ASP cc_start: 0.8598 (t0) cc_final: 0.8066 (t0) REVERT: B 106 ASN cc_start: 0.8786 (t0) cc_final: 0.8168 (t0) REVERT: B 253 SER cc_start: 0.9355 (m) cc_final: 0.8592 (t) REVERT: B 339 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7620 (mm-30) REVERT: A 29 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8759 (tmmt) REVERT: A 104 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7893 (ppp80) REVERT: A 174 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 203 PHE cc_start: 0.7853 (t80) cc_final: 0.7534 (t80) REVERT: A 586 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7543 (mm110) REVERT: A 599 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6798 (pt) REVERT: A 648 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6380 (mt-10) REVERT: A 649 CYS cc_start: 0.7526 (p) cc_final: 0.7258 (p) REVERT: A 656 SER cc_start: 0.8892 (m) cc_final: 0.8571 (p) REVERT: A 741 LEU cc_start: 0.8379 (tt) cc_final: 0.7939 (tt) REVERT: A 817 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5242 (p90) REVERT: A 825 TRP cc_start: 0.8774 (m100) cc_final: 0.8374 (m100) REVERT: A 828 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7787 (mp0) outliers start: 30 outliers final: 21 residues processed: 150 average time/residue: 0.1908 time to fit residues: 41.6221 Evaluate side-chains 147 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108474 restraints weight = 15965.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112087 restraints weight = 8277.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114599 restraints weight = 5281.711| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.214 Angle : 0.731 12.605 12368 Z= 0.355 Chirality : 0.046 0.176 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.113 54.239 1219 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.89 % Favored : 91.02 % Rotamer: Outliers : 2.87 % Allowed : 17.51 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1114 helix: -0.65 (0.24), residues: 454 sheet: -1.48 (0.47), residues: 140 loop : -1.16 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.013 0.001 HIS A 597 PHE 0.016 0.001 PHE A 783 TYR 0.013 0.001 TYR A 27 ARG 0.003 0.000 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.92 seconds wall clock time: 35 minutes 50.49 seconds (2150.49 seconds total)