Starting phenix.real_space_refine on Wed Feb 14 09:22:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/02_2024/6j5w_0683_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/02_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_0683/02_2024/6j5w_0683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/02_2024/6j5w_0683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/02_2024/6j5w_0683_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5w_0683/02_2024/6j5w_0683_updated.pdb" } 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 Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 2 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: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6530 Unusual residues: {'ADP': 1} Classifications: {'peptide': 816, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 788, None: 1} Not linked: pdbres="THR A 847 " pdbres="ADP A 901 " Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.17, per 1000 atoms: 0.58 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 - 3.50 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: 3.51 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 37.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 16 through 38 removed outlier: 3.754A pdb=" N LYS B 20 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 21 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 24 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 25 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 26 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 35 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS B 38 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 98 through 116 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) removed outlier: 4.429A pdb=" N SER B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASN B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 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) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 248 through 263 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 279 through 288 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.603A pdb=" N LEU B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 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 17 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 26 through 41 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 46 through 50 Processing helix chain 'A' and resid 56 through 80 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) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.710A pdb=" N ALA A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.814A pdb=" N LYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 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) removed outlier: 3.573A pdb=" N SER A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.450A pdb=" N ASN A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 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 274 through 281 removed outlier: 3.699A pdb=" N ASP A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 280 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 281 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.949A pdb=" N ASP A 346 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 351 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 353 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 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 376 through 389 removed outlier: 3.703A pdb=" N ILE A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 removed outlier: 3.774A pdb=" N GLN A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 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) removed outlier: 3.978A pdb=" N LEU A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 removed outlier: 3.703A pdb=" N GLY A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 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 489 through 500 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) Processing helix chain 'A' and resid 575 through 583 removed outlier: 4.813A pdb=" N ASP A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU A 581 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 628 through 631 removed outlier: 4.109A pdb=" N VAL A 631 " --> pdb=" O PRO A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 653 through 656 Processing helix chain 'A' and resid 677 through 682 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 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 781 through 784 No H-bonds generated for 'chain 'A' and resid 781 through 784' Processing helix chain 'A' and resid 809 through 814 Processing sheet with id= A, 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= B, first strand: chain 'B' and resid 197 through 199 Processing sheet with id= C, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.705A pdb=" N LEU B 124 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 136 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS B 126 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 134 " --> pdb=" O CYS B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 183 through 188 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) Processing sheet with id= E, 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) Processing sheet with id= F, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.034A pdb=" N ILE A 614 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 638 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 662 " --> pdb=" O LEU A 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 688 through 691 removed outlier: 6.188A pdb=" N SER A 715 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 691 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 717 " --> pdb=" O LEU A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 743 through 746 removed outlier: 6.372A pdb=" N TYR A 768 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU A 746 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER A 770 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 795 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE A 771 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET A 797 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR A 820 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU A 798 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 822 " --> pdb=" O LEU A 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 200 hydrogen bonds defined for protein. 528 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: 2.53 Time building geometry restraints manager: 3.77 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: 98.44 - 105.98: 188 105.98 - 113.52: 5149 113.52 - 121.06: 4480 121.06 - 128.60: 2459 128.60 - 136.14: 92 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: 1741 2.77 - 3.30: 8371 3.30 - 3.83: 14159 3.83 - 4.37: 16575 4.37 - 4.90: 27799 Nonbonded interactions: 68645 Sorted by model distance: nonbonded pdb=" O VAL B 151 " pdb=" OG SER B 158 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASP A 267 " pdb=" OG1 THR A 295 " model vdw 2.278 2.440 nonbonded pdb=" O LEU B 123 " pdb=" OH TYR A 721 " model vdw 2.317 2.440 nonbonded pdb=" OG SER A 773 " pdb=" OG SER A 800 " model vdw 2.339 2.440 nonbonded pdb=" O ASN B 116 " pdb=" OG SER A 773 " model vdw 2.346 2.440 ... (remaining 68640 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 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: 0.210 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: 1.390 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.810 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- 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= 0.506 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 : 1.570 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: 0.2620 time to fit residues: 73.6163 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 142 HIS B 174 ASN B 180 HIS A 42 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 450 ASN A 548 ASN A 643 ASN A 742 HIS A 761 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1857 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= 0.176 Angle : 0.700 12.030 12368 Z= 0.351 Chirality : 0.045 0.171 1391 Planarity : 0.005 0.047 1576 Dihedral : 7.692 57.473 1227 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.84 % Rotamer: Outliers : 3.17 % Allowed : 10.29 % Favored : 86.55 % 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: -3.60 (0.23), residues: 1114 helix: -2.61 (0.19), residues: 435 sheet: -2.72 (0.43), residues: 114 loop : -2.05 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 825 HIS 0.003 0.001 HIS A 597 PHE 0.015 0.001 PHE A 633 TYR 0.027 0.001 TYR A 27 ARG 0.005 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 177 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8290 (t0) cc_final: 0.7973 (t0) REVERT: B 326 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7222 (ptm160) REVERT: B 339 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7575 (mm-30) REVERT: A 29 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8263 (mmtm) REVERT: A 169 LYS cc_start: 0.8315 (mptt) cc_final: 0.7811 (mtmt) REVERT: A 391 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7090 (ptp90) REVERT: A 498 ILE cc_start: 0.9233 (tp) cc_final: 0.8933 (tp) REVERT: A 612 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 622 ASN cc_start: 0.8413 (p0) cc_final: 0.7589 (p0) REVERT: A 634 LYS cc_start: 0.7115 (mppt) cc_final: 0.6708 (mmtt) REVERT: A 828 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7859 (mp0) outliers start: 32 outliers final: 14 residues processed: 170 average time/residue: 0.2244 time to fit residues: 51.9779 Evaluate side-chains 127 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain B residue 304 ILE 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 450 ASN 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 623 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: 2.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN A 42 GLN A 210 HIS ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9154 Z= 0.248 Angle : 0.725 12.013 12368 Z= 0.358 Chirality : 0.047 0.212 1391 Planarity : 0.004 0.043 1576 Dihedral : 7.174 54.131 1221 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.69 % Favored : 90.13 % Rotamer: Outliers : 4.15 % Allowed : 11.67 % Favored : 84.17 % 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: -3.13 (0.24), residues: 1114 helix: -2.09 (0.21), residues: 436 sheet: -2.59 (0.43), residues: 123 loop : -1.85 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 844 HIS 0.006 0.001 HIS A 597 PHE 0.019 0.002 PHE A 633 TYR 0.021 0.002 TYR A 27 ARG 0.004 0.001 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 169 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8229 (t0) cc_final: 0.7949 (t70) REVERT: B 141 GLU cc_start: 0.7688 (pm20) cc_final: 0.7069 (pm20) REVERT: B 269 MET cc_start: 0.5957 (ttt) cc_final: 0.5749 (tmm) REVERT: B 333 MET cc_start: 0.8506 (mmm) cc_final: 0.8229 (tpp) REVERT: B 339 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7659 (mm-30) REVERT: A 169 LYS cc_start: 0.8406 (mptt) cc_final: 0.7840 (mtmt) REVERT: A 498 ILE cc_start: 0.9266 (tp) cc_final: 0.8997 (tp) REVERT: A 612 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8969 (tt) REVERT: A 622 ASN cc_start: 0.8427 (p0) cc_final: 0.7676 (p0) REVERT: A 817 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.5378 (p90) REVERT: A 828 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7935 (mp0) outliers start: 42 outliers final: 24 residues processed: 158 average time/residue: 0.2398 time to fit residues: 52.5800 Evaluate side-chains 133 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 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 326 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 MET 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 450 ASN 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 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: 0.0000 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9154 Z= 0.168 Angle : 0.658 11.831 12368 Z= 0.325 Chirality : 0.045 0.170 1391 Planarity : 0.004 0.041 1576 Dihedral : 6.735 51.355 1221 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.89 % Favored : 91.02 % Rotamer: Outliers : 3.66 % Allowed : 12.96 % Favored : 83.38 % 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: -2.63 (0.25), residues: 1114 helix: -1.64 (0.22), residues: 436 sheet: -2.44 (0.44), residues: 120 loop : -1.57 (0.29), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 277 HIS 0.004 0.001 HIS A 597 PHE 0.014 0.001 PHE A 633 TYR 0.018 0.001 TYR A 27 ARG 0.003 0.000 ARG A 695 *********************** 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 171 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8212 (t0) cc_final: 0.7774 (t0) REVERT: B 113 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7971 (ttp-170) REVERT: B 269 MET cc_start: 0.6317 (ttt) cc_final: 0.6045 (ptm) REVERT: B 333 MET cc_start: 0.8432 (mmm) cc_final: 0.8076 (tpp) REVERT: B 339 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7661 (mm-30) REVERT: A 64 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (t0) REVERT: A 169 LYS cc_start: 0.8379 (mptt) cc_final: 0.7769 (mtmt) REVERT: A 391 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6657 (ptp90) REVERT: A 498 ILE cc_start: 0.9273 (tp) cc_final: 0.9058 (tp) REVERT: A 599 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6555 (pt) REVERT: A 612 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 622 ASN cc_start: 0.8295 (p0) cc_final: 0.7517 (p0) REVERT: A 817 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.5213 (p90) REVERT: A 828 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7953 (mp0) outliers start: 37 outliers final: 23 residues processed: 157 average time/residue: 0.2236 time to fit residues: 48.2530 Evaluate side-chains 144 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 326 ARG 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 152 SER Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 MET 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 475 ASP Chi-restraints excluded: chain A residue 517 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.0470 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3018 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= 0.164 Angle : 0.639 11.375 12368 Z= 0.317 Chirality : 0.044 0.160 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.413 49.338 1221 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 3.66 % Allowed : 13.45 % Favored : 82.89 % 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: -2.20 (0.26), residues: 1114 helix: -1.22 (0.24), residues: 431 sheet: -2.27 (0.45), residues: 121 loop : -1.36 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS A 597 PHE 0.031 0.001 PHE B 139 TYR 0.016 0.001 TYR A 27 ARG 0.003 0.000 ARG B 82 *********************** 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 170 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 MET cc_start: 0.6247 (ttt) cc_final: 0.5568 (ptm) REVERT: B 333 MET cc_start: 0.8364 (mmm) cc_final: 0.7999 (tpp) REVERT: B 339 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7657 (mm-30) REVERT: A 29 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8423 (mmtm) REVERT: A 150 TRP cc_start: 0.7459 (m-90) cc_final: 0.7244 (m-90) REVERT: A 169 LYS cc_start: 0.8339 (mptt) cc_final: 0.7761 (mtmt) REVERT: A 391 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6518 (ptp90) REVERT: A 568 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8427 (mtmm) REVERT: A 599 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6457 (pt) REVERT: A 622 ASN cc_start: 0.8035 (p0) cc_final: 0.7336 (p0) REVERT: A 649 CYS cc_start: 0.7521 (p) cc_final: 0.7297 (p) REVERT: A 817 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5144 (p90) REVERT: A 828 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7879 (mp0) outliers start: 37 outliers final: 24 residues processed: 157 average time/residue: 0.2112 time to fit residues: 45.8967 Evaluate side-chains 137 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 152 SER Chi-restraints excluded: chain A residue 230 MET 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 475 ASP Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 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 763 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: 1.9990 chunk 26 optimal weight: 0.0870 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3171 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= 0.206 Angle : 0.649 11.311 12368 Z= 0.321 Chirality : 0.045 0.154 1391 Planarity : 0.004 0.040 1576 Dihedral : 6.243 50.564 1219 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.16 % Favored : 90.75 % Rotamer: Outliers : 4.45 % Allowed : 13.65 % Favored : 81.90 % 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: -2.02 (0.26), residues: 1114 helix: -1.05 (0.25), residues: 426 sheet: -2.13 (0.45), residues: 131 loop : -1.27 (0.30), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.004 0.001 HIS A 597 PHE 0.023 0.001 PHE B 139 TYR 0.015 0.001 TYR A 27 ARG 0.003 0.000 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 166 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.8452 (t0) cc_final: 0.8187 (t0) REVERT: B 185 LYS cc_start: 0.8708 (pttp) cc_final: 0.8338 (pttp) REVERT: B 195 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8511 (mmm) REVERT: B 269 MET cc_start: 0.6233 (ttt) cc_final: 0.6026 (ptm) REVERT: B 333 MET cc_start: 0.8389 (mmm) cc_final: 0.8188 (mmm) REVERT: B 339 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7562 (mm-30) REVERT: A 209 GLU cc_start: 0.8433 (tt0) cc_final: 0.8229 (tt0) REVERT: A 391 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6473 (ptp90) REVERT: A 599 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6500 (pt) REVERT: A 622 ASN cc_start: 0.7997 (p0) cc_final: 0.7228 (p0) REVERT: A 649 CYS cc_start: 0.7603 (p) cc_final: 0.7388 (p) REVERT: A 817 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5257 (p90) REVERT: A 825 TRP cc_start: 0.8965 (m100) cc_final: 0.8492 (m100) REVERT: A 828 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7890 (mp0) outliers start: 45 outliers final: 27 residues processed: 149 average time/residue: 0.2007 time to fit residues: 42.9868 Evaluate side-chains 143 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 195 MET 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 326 ARG 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 230 MET 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 450 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 ASP 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 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 776 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: 0.0570 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9154 Z= 0.160 Angle : 0.657 12.004 12368 Z= 0.321 Chirality : 0.044 0.170 1391 Planarity : 0.004 0.039 1576 Dihedral : 6.044 49.535 1219 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 3.86 % Allowed : 14.24 % Favored : 81.90 % 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: -1.84 (0.26), residues: 1114 helix: -0.96 (0.25), residues: 438 sheet: -1.94 (0.47), residues: 121 loop : -1.15 (0.30), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS A 597 PHE 0.013 0.001 PHE A 633 TYR 0.014 0.001 TYR A 27 ARG 0.003 0.000 ARG A 215 *********************** 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 165 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 1.097 Fit side-chains REVERT: B 37 ASP cc_start: 0.8464 (t0) cc_final: 0.8041 (t0) REVERT: B 145 MET cc_start: 0.7379 (ttt) cc_final: 0.7067 (ttt) REVERT: B 185 LYS cc_start: 0.8679 (pttp) cc_final: 0.8371 (pttp) REVERT: B 195 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8526 (mmm) REVERT: B 253 SER cc_start: 0.9305 (m) cc_final: 0.8499 (t) REVERT: B 339 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7546 (mm-30) REVERT: A 209 GLU cc_start: 0.8411 (tt0) cc_final: 0.8203 (tt0) REVERT: A 599 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6877 (pt) REVERT: A 649 CYS cc_start: 0.7617 (p) cc_final: 0.7409 (p) REVERT: A 817 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5065 (p90) REVERT: A 825 TRP cc_start: 0.8898 (m100) cc_final: 0.8519 (m100) REVERT: A 828 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7890 (mp0) outliers start: 39 outliers final: 25 residues processed: 151 average time/residue: 0.2004 time to fit residues: 43.0695 Evaluate side-chains 146 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 195 MET 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 152 SER Chi-restraints excluded: chain A residue 230 MET 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 450 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 505 SER 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 623 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 817 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.0000 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9154 Z= 0.159 Angle : 0.654 12.913 12368 Z= 0.319 Chirality : 0.044 0.157 1391 Planarity : 0.004 0.039 1576 Dihedral : 5.871 49.497 1219 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.16 % Favored : 90.75 % Rotamer: Outliers : 3.46 % Allowed : 14.94 % Favored : 81.60 % 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: -1.69 (0.27), residues: 1114 helix: -0.81 (0.25), residues: 439 sheet: -1.81 (0.48), residues: 121 loop : -1.11 (0.30), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 150 HIS 0.003 0.000 HIS A 597 PHE 0.015 0.001 PHE A 783 TYR 0.013 0.001 TYR A 27 ARG 0.004 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 160 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 0.982 Fit side-chains REVERT: B 37 ASP cc_start: 0.8583 (t0) cc_final: 0.8256 (t0) REVERT: B 68 GLN cc_start: 0.8287 (pp30) cc_final: 0.7983 (pp30) REVERT: B 145 MET cc_start: 0.7254 (ttt) cc_final: 0.6824 (ttt) REVERT: B 253 SER cc_start: 0.9302 (m) cc_final: 0.8522 (t) REVERT: B 339 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7559 (mm-30) REVERT: A 599 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6812 (pt) REVERT: A 649 CYS cc_start: 0.7616 (p) cc_final: 0.7359 (p) REVERT: A 817 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.5024 (p90) REVERT: A 825 TRP cc_start: 0.8834 (m100) cc_final: 0.8460 (m100) REVERT: A 828 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7891 (mp0) outliers start: 35 outliers final: 25 residues processed: 144 average time/residue: 0.1907 time to fit residues: 39.5674 Evaluate side-chains 141 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 153 VAL 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 152 SER Chi-restraints excluded: chain A residue 230 MET 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 419 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 505 SER 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 686 LEU Chi-restraints excluded: chain A residue 744 LEU 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: 0.5980 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9154 Z= 0.162 Angle : 0.670 11.916 12368 Z= 0.326 Chirality : 0.045 0.304 1391 Planarity : 0.004 0.040 1576 Dihedral : 5.803 50.090 1219 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.89 % Favored : 91.02 % Rotamer: Outliers : 2.97 % Allowed : 15.63 % Favored : 81.40 % 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 (0.27), residues: 1114 helix: -0.75 (0.25), residues: 436 sheet: -1.64 (0.49), residues: 121 loop : -1.12 (0.30), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 150 HIS 0.003 0.000 HIS A 597 PHE 0.018 0.001 PHE A 783 TYR 0.014 0.001 TYR B 71 ARG 0.007 0.000 ARG A 449 *********************** 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: 30 poor density : 127 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7528 (pm20) cc_final: 0.6309 (tm-30) REVERT: B 253 SER cc_start: 0.9294 (m) cc_final: 0.8503 (t) REVERT: B 339 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7530 (mm-30) REVERT: A 599 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6708 (pt) REVERT: A 649 CYS cc_start: 0.7566 (p) cc_final: 0.7309 (p) REVERT: A 817 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.4948 (p90) REVERT: A 825 TRP cc_start: 0.8752 (m100) cc_final: 0.8401 (m100) REVERT: A 828 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7871 (mp0) outliers start: 30 outliers final: 23 residues processed: 143 average time/residue: 0.1962 time to fit residues: 40.2771 Evaluate side-chains 139 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 108 ILE 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 152 SER Chi-restraints excluded: chain A residue 230 MET 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 475 ASP Chi-restraints excluded: chain A residue 505 SER 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 744 LEU 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: 6.9990 chunk 73 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9154 Z= 0.175 Angle : 0.672 11.976 12368 Z= 0.328 Chirality : 0.045 0.263 1391 Planarity : 0.004 0.039 1576 Dihedral : 5.773 50.704 1219 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 2.77 % Allowed : 15.92 % Favored : 81.31 % 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 (0.27), residues: 1114 helix: -0.70 (0.25), residues: 437 sheet: -1.44 (0.50), residues: 121 loop : -1.14 (0.30), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 150 HIS 0.004 0.001 HIS A 597 PHE 0.018 0.001 PHE A 783 TYR 0.013 0.001 TYR A 27 ARG 0.003 0.000 ARG A 28 ********************** 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 150 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7506 (pm20) cc_final: 0.6284 (tm-30) REVERT: B 253 SER cc_start: 0.9312 (m) cc_final: 0.8510 (t) REVERT: B 339 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7660 (mm-30) REVERT: A 1 MET cc_start: 0.8219 (pmm) cc_final: 0.7893 (pmm) REVERT: A 29 LYS cc_start: 0.9125 (tmmt) cc_final: 0.8863 (tmmt) REVERT: A 599 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6704 (pt) REVERT: A 649 CYS cc_start: 0.7517 (p) cc_final: 0.7149 (p) REVERT: A 817 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5128 (p90) REVERT: A 825 TRP cc_start: 0.8746 (m100) cc_final: 0.8325 (m100) REVERT: A 828 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7783 (mp0) outliers start: 28 outliers final: 23 residues processed: 138 average time/residue: 0.2120 time to fit residues: 42.3647 Evaluate side-chains 139 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ILE 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 249 THR Chi-restraints excluded: chain B residue 326 ARG 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 460 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 505 SER 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 686 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL 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: 9.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112915 restraints weight = 15672.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116603 restraints weight = 8102.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119155 restraints weight = 5090.347| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9154 Z= 0.164 Angle : 0.670 12.459 12368 Z= 0.324 Chirality : 0.045 0.304 1391 Planarity : 0.003 0.038 1576 Dihedral : 5.648 50.738 1219 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.44 % Favored : 91.47 % Rotamer: Outliers : 2.77 % Allowed : 16.02 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.47 (0.27), residues: 1114 helix: -0.63 (0.25), residues: 438 sheet: -1.39 (0.51), residues: 121 loop : -1.06 (0.30), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.003 0.001 HIS A 157 PHE 0.019 0.001 PHE A 783 TYR 0.012 0.001 TYR A 27 ARG 0.002 0.000 ARG A 695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.18 seconds wall clock time: 37 minutes 17.45 seconds (2237.45 seconds total)