Starting phenix.real_space_refine (version: dev) on Sun Feb 19 15:47:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/02_2023/7sck_25037_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.036 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 Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5239 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 608} Chain breaks: 1 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4854 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 558} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BDP': 2, 'NDG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.44, per 1000 atoms: 0.63 Number of scatterers: 10250 At special positions: 0 Unit cell: (110.124, 88.596, 110.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 48 16.00 P 4 15.00 O 1894 8.00 N 1720 7.00 C 6583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 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 Links applied ALPHA1-4 " BDP D 2 " - " NDG D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NDG D 1 " - " BDP D 2 " " NDG D 3 " - " BDP D 4 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 12 sheets defined 30.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.123A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.630A pdb=" N HIS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.733A pdb=" N ARG A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.580A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.793A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 696 through 712 Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.832A pdb=" N GLU B 239 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.802A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 314' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.537A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.925A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.658A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 669 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.271A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.950A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 217 " --> pdb=" O ASN A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 269 Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.052A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 623 through 627 removed outlier: 7.497A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 515 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 537 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TRP A 517 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 539 " --> pdb=" O TRP A 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 596 through 600 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.299A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.687A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.391A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 317 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N SER B 257 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 319 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= K, first strand: chain 'B' and resid 563 through 565 removed outlier: 3.806A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 570 through 574 238 hydrogen bonds defined for protein. 675 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: 2.89 Time building geometry restraints manager: 5.06 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: 2584 1.33 - 1.45: 2239 1.45 - 1.58: 5626 1.58 - 1.70: 5 1.70 - 1.82: 74 Bond restraints: 10528 Sorted by residual: bond pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 1.458 1.499 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N TYR B 566 " pdb=" CA TYR B 566 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.41e-02 5.03e+03 7.62e+00 bond pdb=" N GLN A 677 " pdb=" CA GLN A 677 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.22e-02 6.72e+03 7.22e+00 bond pdb=" C LEU B 563 " pdb=" N VAL B 564 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.05e-02 9.07e+03 6.15e+00 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.77: 395 106.77 - 113.58: 5725 113.58 - 120.39: 3867 120.39 - 127.20: 4175 127.20 - 134.00: 150 Bond angle restraints: 14312 Sorted by residual: angle pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3A UDP B 901 " ideal model delta sigma weight residual 102.95 112.07 -9.12 1.00e+00 1.00e+00 8.33e+01 angle pdb=" O3A UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3B UDP B 901 " ideal model delta sigma weight residual 112.01 103.15 8.86 1.00e+00 1.00e+00 7.86e+01 angle pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N ARG B 562 " pdb=" CA ARG B 562 " pdb=" CB ARG B 562 " ideal model delta sigma weight residual 110.49 104.68 5.81 1.69e+00 3.50e-01 1.18e+01 angle pdb=" C PRO B 560 " pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 122.49 117.30 5.19 1.57e+00 4.06e-01 1.09e+01 ... (remaining 14307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 6024 20.49 - 40.98: 219 40.98 - 61.46: 22 61.46 - 81.95: 3 81.95 - 102.44: 3 Dihedral angle restraints: 6271 sinusoidal: 2601 harmonic: 3670 Sorted by residual: dihedral pdb=" C1 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O5 NDG D 3 " pdb=" C6 NDG D 3 " ideal model delta sinusoidal sigma weight residual 179.69 -77.87 -102.44 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -113.01 27.01 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CA ARG B 166 " pdb=" C ARG B 166 " pdb=" N ILE B 167 " pdb=" CA ILE B 167 " ideal model delta harmonic sigma weight residual 180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 6268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1174 0.045 - 0.091: 307 0.091 - 0.136: 86 0.136 - 0.182: 1 0.182 - 0.227: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ARG B 562 " pdb=" N ARG B 562 " pdb=" C ARG B 562 " pdb=" CB ARG B 562 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE B 380 " pdb=" N ILE B 380 " pdb=" C ILE B 380 " pdb=" CB ILE B 380 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1567 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 561 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP B 561 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 561 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 562 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.025 2.00e-02 2.50e+03 1.31e-02 3.41e+00 pdb=" CG TYR B 399 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 480 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 26 2.38 - 3.01: 5753 3.01 - 3.64: 15481 3.64 - 4.27: 24123 4.27 - 4.90: 40229 Nonbonded interactions: 85612 Sorted by model distance: nonbonded pdb=" O2A UDP B 901 " pdb="MN MN B 902 " model vdw 1.744 2.320 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.229 2.440 nonbonded pdb=" NZ LYS B 484 " pdb=" O GLU B 528 " model vdw 2.241 2.520 nonbonded pdb=" O ARG B 209 " pdb=" OH TYR B 226 " model vdw 2.241 2.440 nonbonded pdb=" N ASP B 539 " pdb=" OD1 ASP B 539 " model vdw 2.252 2.520 ... (remaining 85607 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 4 5.49 5 S 48 5.16 5 C 6583 2.51 5 N 1720 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.160 Process input model: 30.480 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.004 0.040 10528 Z= 0.260 Angle : 0.565 9.125 14312 Z= 0.318 Chirality : 0.043 0.227 1570 Planarity : 0.004 0.042 1806 Dihedral : 10.381 102.440 3872 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1228 helix: 0.91 (0.28), residues: 382 sheet: -0.17 (0.48), residues: 122 loop : -0.60 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 339 average time/residue: 1.1448 time to fit residues: 418.7076 Evaluate side-chains 264 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1502 time to fit residues: 1.9259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 378 GLN B 430 ASN B 490 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10528 Z= 0.218 Angle : 0.589 7.683 14312 Z= 0.290 Chirality : 0.044 0.218 1570 Planarity : 0.005 0.050 1806 Dihedral : 5.930 102.270 1411 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1228 helix: 0.69 (0.27), residues: 383 sheet: -0.08 (0.49), residues: 115 loop : -0.50 (0.23), residues: 730 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 284 average time/residue: 1.2018 time to fit residues: 368.6804 Evaluate side-chains 269 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 6 average time/residue: 0.1757 time to fit residues: 3.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 550 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10528 Z= 0.210 Angle : 0.582 7.330 14312 Z= 0.285 Chirality : 0.044 0.224 1570 Planarity : 0.004 0.047 1806 Dihedral : 5.934 102.177 1411 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1228 helix: 0.58 (0.27), residues: 389 sheet: -0.21 (0.46), residues: 137 loop : -0.61 (0.24), residues: 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 283 average time/residue: 1.1658 time to fit residues: 357.4030 Evaluate side-chains 280 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 8 residues processed: 11 average time/residue: 0.5905 time to fit residues: 9.2464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10528 Z= 0.275 Angle : 0.618 7.854 14312 Z= 0.303 Chirality : 0.045 0.247 1570 Planarity : 0.004 0.049 1806 Dihedral : 6.033 101.339 1411 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1228 helix: 0.45 (0.26), residues: 389 sheet: -0.22 (0.46), residues: 135 loop : -0.67 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 272 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 288 average time/residue: 1.1641 time to fit residues: 361.8328 Evaluate side-chains 277 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 8 average time/residue: 0.3349 time to fit residues: 5.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10528 Z= 0.212 Angle : 0.607 9.330 14312 Z= 0.295 Chirality : 0.044 0.236 1570 Planarity : 0.004 0.054 1806 Dihedral : 5.966 101.947 1411 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1228 helix: 0.51 (0.26), residues: 388 sheet: -0.25 (0.46), residues: 135 loop : -0.64 (0.24), residues: 705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 264 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 281 average time/residue: 1.1788 time to fit residues: 358.2523 Evaluate side-chains 278 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 10 average time/residue: 0.6114 time to fit residues: 8.6180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 490 ASN B 517 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10528 Z= 0.262 Angle : 0.619 11.369 14312 Z= 0.302 Chirality : 0.045 0.247 1570 Planarity : 0.004 0.051 1806 Dihedral : 6.012 101.487 1411 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1228 helix: 0.41 (0.26), residues: 389 sheet: -0.33 (0.48), residues: 125 loop : -0.62 (0.24), residues: 714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 279 average time/residue: 1.1607 time to fit residues: 349.6175 Evaluate side-chains 276 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 12 average time/residue: 0.2941 time to fit residues: 6.4554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 72 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 490 ASN B 517 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10528 Z= 0.235 Angle : 0.634 8.360 14312 Z= 0.311 Chirality : 0.046 0.237 1570 Planarity : 0.005 0.058 1806 Dihedral : 6.066 101.724 1411 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1228 helix: 0.42 (0.26), residues: 388 sheet: -0.41 (0.48), residues: 127 loop : -0.63 (0.24), residues: 713 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 278 average time/residue: 1.1917 time to fit residues: 358.1368 Evaluate side-chains 272 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 8 average time/residue: 0.6197 time to fit residues: 7.4582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 517 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 10528 Z= 0.282 Angle : 0.656 10.035 14312 Z= 0.322 Chirality : 0.046 0.245 1570 Planarity : 0.005 0.052 1806 Dihedral : 6.129 101.388 1411 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1228 helix: 0.33 (0.26), residues: 388 sheet: -0.42 (0.48), residues: 124 loop : -0.69 (0.24), residues: 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 254 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 273 average time/residue: 1.2421 time to fit residues: 365.9779 Evaluate side-chains 272 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 8 average time/residue: 0.6389 time to fit residues: 7.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0000 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 517 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10528 Z= 0.225 Angle : 0.646 9.982 14312 Z= 0.314 Chirality : 0.045 0.229 1570 Planarity : 0.005 0.055 1806 Dihedral : 6.003 101.952 1411 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1228 helix: 0.41 (0.27), residues: 382 sheet: -0.37 (0.48), residues: 124 loop : -0.69 (0.24), residues: 722 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 274 average time/residue: 1.1881 time to fit residues: 351.5558 Evaluate side-chains 275 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 256 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 6 average time/residue: 0.4160 time to fit residues: 4.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10528 Z= 0.219 Angle : 0.645 9.926 14312 Z= 0.315 Chirality : 0.045 0.229 1570 Planarity : 0.004 0.052 1806 Dihedral : 5.941 102.244 1411 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1228 helix: 0.40 (0.26), residues: 385 sheet: -0.36 (0.48), residues: 126 loop : -0.67 (0.24), residues: 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 266 average time/residue: 1.1501 time to fit residues: 330.5180 Evaluate side-chains 265 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 0.1819 time to fit residues: 2.5406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.156644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139060 restraints weight = 13886.178| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.11 r_work: 0.3815 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10528 Z= 0.211 Angle : 0.654 11.292 14312 Z= 0.319 Chirality : 0.044 0.218 1570 Planarity : 0.004 0.051 1806 Dihedral : 5.892 102.716 1411 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1228 helix: 0.42 (0.27), residues: 385 sheet: -0.29 (0.48), residues: 126 loop : -0.60 (0.24), residues: 717 =============================================================================== Job complete usr+sys time: 5516.65 seconds wall clock time: 98 minutes 39.38 seconds (5919.38 seconds total)