Starting phenix.real_space_refine on Thu Mar 14 13:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avw_15685/03_2024/8avw_15685_updated.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5706 2.51 5 N 1602 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4448 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 531} Chain breaks: 2 Chain: "B" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 533} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.57 Number of scatterers: 8992 At special positions: 0 Unit cell: (93.9253, 98.2338, 174.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1660 8.00 N 1602 7.00 C 5706 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: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 36.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.764A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.535A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.713A pdb=" N GLN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 4.220A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.673A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.741A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.634A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 532 removed outlier: 3.971A pdb=" N LEU A 506 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 507 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 508 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 510 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 515 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 516 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 517 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 519 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 520 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 522 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 523 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 526 " --> pdb=" O TRP A 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 527 " --> pdb=" O ARG A 524 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 529 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE A 530 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 531 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 547 through 550 No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 564 through 590 removed outlier: 3.827A pdb=" N ARG A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.766A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.544A pdb=" N PHE B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.713A pdb=" N GLN B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 330 removed outlier: 4.199A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.687A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.744A pdb=" N ASP B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 485 through 498 removed outlier: 3.638A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 533 removed outlier: 3.970A pdb=" N LEU B 506 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 507 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 508 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B 510 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 512 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 515 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 516 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 517 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 520 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 522 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 523 " --> pdb=" O ASN B 520 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 524 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 526 " --> pdb=" O TRP B 523 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY B 527 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 529 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE B 530 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 531 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 564 through 590 removed outlier: 3.833A pdb=" N ARG B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 574 " --> pdb=" O PHE B 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 98 through 103 removed outlier: 3.609A pdb=" N LEU A 111 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 53 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.881A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS A 290 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 271 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 222 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 375 through 380 removed outlier: 4.101A pdb=" N PHE A 372 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 447 through 452 removed outlier: 4.010A pdb=" N LEU A 447 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 98 through 103 removed outlier: 3.612A pdb=" N LEU B 111 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 53 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP B 45 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 51 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.881A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 290 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 271 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 222 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 375 through 380 removed outlier: 4.102A pdb=" N PHE B 372 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 447 through 452 removed outlier: 4.003A pdb=" N LEU B 447 " --> pdb=" O LYS B 476 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 792 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: 2.62 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1910 1.34 - 1.46: 3087 1.46 - 1.58: 4186 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 9223 Sorted by residual: bond pdb=" C2D LBV A1000 " pdb=" C3D LBV A1000 " ideal model delta sigma weight residual 1.358 1.432 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C2D LBV B1000 " pdb=" C3D LBV B1000 " ideal model delta sigma weight residual 1.358 1.430 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4C LBV A1000 " pdb=" CHD LBV A1000 " ideal model delta sigma weight residual 1.428 1.357 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4C LBV B1000 " pdb=" CHD LBV B1000 " ideal model delta sigma weight residual 1.428 1.359 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C SER B 558 " pdb=" N PRO B 559 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.12e+01 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.46: 449 106.46 - 113.46: 4723 113.46 - 120.47: 3792 120.47 - 127.47: 3545 127.47 - 134.48: 102 Bond angle restraints: 12611 Sorted by residual: angle pdb=" N GLN A 329 " pdb=" CA GLN A 329 " pdb=" C GLN A 329 " ideal model delta sigma weight residual 114.04 108.55 5.49 1.24e+00 6.50e-01 1.96e+01 angle pdb=" N GLN B 329 " pdb=" CA GLN B 329 " pdb=" C GLN B 329 " ideal model delta sigma weight residual 114.04 108.56 5.48 1.24e+00 6.50e-01 1.95e+01 angle pdb=" N LEU B 360 " pdb=" CA LEU B 360 " pdb=" C LEU B 360 " ideal model delta sigma weight residual 114.56 109.47 5.09 1.27e+00 6.20e-01 1.61e+01 angle pdb=" N LEU A 360 " pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 114.56 109.55 5.01 1.27e+00 6.20e-01 1.55e+01 angle pdb=" C LEU B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta sigma weight residual 119.66 122.52 -2.86 7.30e-01 1.88e+00 1.54e+01 ... (remaining 12606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 4637 15.85 - 31.71: 575 31.71 - 47.56: 176 47.56 - 63.41: 99 63.41 - 79.27: 32 Dihedral angle restraints: 5519 sinusoidal: 2210 harmonic: 3309 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C ASN A 243 " pdb=" N ASN A 243 " pdb=" CA ASN A 243 " pdb=" CB ASN A 243 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 5516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 771 0.058 - 0.116: 394 0.116 - 0.175: 186 0.175 - 0.233: 48 0.233 - 0.291: 13 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA GLN B 551 " pdb=" N GLN B 551 " pdb=" C GLN B 551 " pdb=" CB GLN B 551 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1409 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C LBV A1000 " 0.063 2.00e-02 2.50e+03 2.16e-01 1.05e+03 pdb=" C2C LBV A1000 " -0.100 2.00e-02 2.50e+03 pdb=" C3C LBV A1000 " 0.083 2.00e-02 2.50e+03 pdb=" C4C LBV A1000 " -0.068 2.00e-02 2.50e+03 pdb=" CAC LBV A1000 " -0.376 2.00e-02 2.50e+03 pdb=" CHC LBV A1000 " 0.254 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.218 2.00e-02 2.50e+03 pdb=" CMC LBV A1000 " 0.377 2.00e-02 2.50e+03 pdb=" N_C LBV A1000 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C LBV B1000 " 0.052 2.00e-02 2.50e+03 1.63e-01 5.97e+02 pdb=" C2C LBV B1000 " -0.073 2.00e-02 2.50e+03 pdb=" C3C LBV B1000 " 0.063 2.00e-02 2.50e+03 pdb=" C4C LBV B1000 " -0.054 2.00e-02 2.50e+03 pdb=" CAC LBV B1000 " -0.282 2.00e-02 2.50e+03 pdb=" CHC LBV B1000 " 0.173 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " -0.181 2.00e-02 2.50e+03 pdb=" CMC LBV B1000 " 0.286 2.00e-02 2.50e+03 pdb=" N_C LBV B1000 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D LBV B1000 " -0.010 2.00e-02 2.50e+03 1.47e-01 4.89e+02 pdb=" C2D LBV B1000 " -0.044 2.00e-02 2.50e+03 pdb=" C3D LBV B1000 " 0.014 2.00e-02 2.50e+03 pdb=" C4D LBV B1000 " -0.035 2.00e-02 2.50e+03 pdb=" CAD LBV B1000 " 0.102 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " 0.257 2.00e-02 2.50e+03 pdb=" CMD LBV B1000 " -0.102 2.00e-02 2.50e+03 pdb=" N_D LBV B1000 " -0.301 2.00e-02 2.50e+03 pdb=" O_D LBV B1000 " 0.121 2.00e-02 2.50e+03 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 4057 3.06 - 3.52: 9144 3.52 - 3.98: 13477 3.98 - 4.44: 15506 4.44 - 4.90: 25185 Nonbonded interactions: 67369 Sorted by model distance: nonbonded pdb=" O GLY A 527 " pdb=" OG1 THR B 589 " model vdw 2.602 2.440 nonbonded pdb=" N ALA B 356 " pdb=" N LEU B 357 " model vdw 2.606 2.560 nonbonded pdb=" N ALA A 356 " pdb=" N LEU A 357 " model vdw 2.607 2.560 nonbonded pdb=" N GLY A 270 " pdb=" O HIS A 291 " model vdw 2.610 2.520 nonbonded pdb=" N GLY B 270 " pdb=" O HIS B 291 " model vdw 2.611 2.520 ... (remaining 67364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 7 through 106 or resid 109 through 591 or resid 1000)) } 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: 5.810 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: 18.350 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.120 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.074 9223 Z= 0.498 Angle : 1.383 6.790 12611 Z= 0.934 Chirality : 0.084 0.291 1412 Planarity : 0.010 0.216 1657 Dihedral : 18.216 79.266 3383 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 3.45 % Allowed : 12.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -4.09 (0.19), residues: 1146 helix: -4.02 (0.14), residues: 436 sheet: 0.01 (0.35), residues: 178 loop : -2.44 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 284 HIS 0.008 0.001 HIS B 335 PHE 0.014 0.002 PHE A 145 TYR 0.017 0.002 TYR A 588 ARG 0.006 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8239 (mm) cc_final: 0.7799 (mm) REVERT: A 45 ASP cc_start: 0.8033 (t70) cc_final: 0.7510 (t0) REVERT: A 222 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8065 (pmm150) REVERT: A 444 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: A 476 LYS cc_start: 0.7886 (mttt) cc_final: 0.7002 (mttp) REVERT: A 479 TYR cc_start: 0.8608 (m-80) cc_final: 0.7193 (m-80) REVERT: A 489 GLU cc_start: 0.9119 (tt0) cc_final: 0.8716 (tp30) REVERT: A 522 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8374 (tm-30) REVERT: A 526 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7124 (t80) REVERT: A 588 TYR cc_start: 0.7104 (m-80) cc_final: 0.6670 (m-80) REVERT: B 24 CYS cc_start: 0.8689 (p) cc_final: 0.8338 (p) REVERT: B 381 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8509 (mp0) REVERT: B 477 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7820 (ptp90) REVERT: B 512 LEU cc_start: 0.8810 (mt) cc_final: 0.8524 (tp) REVERT: B 524 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8757 (tpp-160) REVERT: B 526 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7776 (t80) outliers start: 32 outliers final: 5 residues processed: 150 average time/residue: 0.2549 time to fit residues: 50.6309 Evaluate side-chains 79 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 526 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS B 72 GLN B 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9223 Z= 0.189 Angle : 0.638 8.709 12611 Z= 0.320 Chirality : 0.041 0.135 1412 Planarity : 0.004 0.030 1657 Dihedral : 7.295 64.297 1322 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.01 % Favored : 97.82 % Rotamer: Outliers : 2.26 % Allowed : 17.24 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.46 (0.22), residues: 1146 helix: -2.41 (0.19), residues: 432 sheet: 0.71 (0.39), residues: 164 loop : -1.63 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 284 HIS 0.013 0.001 HIS A 47 PHE 0.012 0.001 PHE B 469 TYR 0.018 0.002 TYR B 176 ARG 0.006 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8783 (mm110) REVERT: A 476 LYS cc_start: 0.7725 (mttt) cc_final: 0.7000 (mttp) REVERT: A 479 TYR cc_start: 0.8485 (m-80) cc_final: 0.7494 (m-80) REVERT: A 489 GLU cc_start: 0.9014 (tt0) cc_final: 0.8624 (tp30) REVERT: A 522 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8546 (tm-30) REVERT: A 526 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 588 TYR cc_start: 0.7075 (m-80) cc_final: 0.6616 (m-80) REVERT: B 24 CYS cc_start: 0.8621 (p) cc_final: 0.8360 (p) REVERT: B 512 LEU cc_start: 0.8956 (mt) cc_final: 0.8754 (tt) REVERT: B 524 ARG cc_start: 0.9157 (mtt180) cc_final: 0.8928 (mmt-90) REVERT: B 526 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7777 (t80) outliers start: 21 outliers final: 6 residues processed: 92 average time/residue: 0.2318 time to fit residues: 29.1864 Evaluate side-chains 73 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS B 262 GLN B 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9223 Z= 0.212 Angle : 0.577 8.824 12611 Z= 0.286 Chirality : 0.041 0.132 1412 Planarity : 0.004 0.043 1657 Dihedral : 6.418 63.296 1313 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.86 % Rotamer: Outliers : 2.16 % Allowed : 16.92 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1146 helix: -1.49 (0.22), residues: 444 sheet: 1.07 (0.41), residues: 163 loop : -1.25 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 523 HIS 0.005 0.001 HIS B 38 PHE 0.010 0.001 PHE A 570 TYR 0.017 0.002 TYR B 472 ARG 0.006 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8745 (mm110) REVERT: A 476 LYS cc_start: 0.7756 (mttt) cc_final: 0.7241 (mttp) REVERT: A 479 TYR cc_start: 0.8413 (m-80) cc_final: 0.8213 (m-80) REVERT: A 489 GLU cc_start: 0.8948 (tt0) cc_final: 0.8611 (tp30) REVERT: A 522 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8313 (tm-30) REVERT: A 526 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.6328 (t80) REVERT: A 588 TYR cc_start: 0.6951 (m-80) cc_final: 0.6510 (m-80) REVERT: B 24 CYS cc_start: 0.8610 (p) cc_final: 0.8349 (p) REVERT: B 512 LEU cc_start: 0.8920 (mt) cc_final: 0.8659 (tp) REVERT: B 523 TRP cc_start: 0.7275 (t60) cc_final: 0.6431 (t60) REVERT: B 526 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7926 (t80) outliers start: 20 outliers final: 10 residues processed: 82 average time/residue: 0.2251 time to fit residues: 25.6334 Evaluate side-chains 76 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9223 Z= 0.202 Angle : 0.551 8.414 12611 Z= 0.269 Chirality : 0.041 0.138 1412 Planarity : 0.004 0.040 1657 Dihedral : 6.230 63.971 1313 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 2.91 % Allowed : 17.46 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1146 helix: -0.96 (0.23), residues: 450 sheet: 0.80 (0.39), residues: 184 loop : -0.92 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 523 HIS 0.005 0.001 HIS B 38 PHE 0.012 0.001 PHE A 544 TYR 0.018 0.002 TYR B 472 ARG 0.004 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8603 (mm-40) REVERT: A 476 LYS cc_start: 0.7768 (mttt) cc_final: 0.7201 (mttp) REVERT: A 479 TYR cc_start: 0.8492 (m-80) cc_final: 0.8290 (m-80) REVERT: A 489 GLU cc_start: 0.8977 (tt0) cc_final: 0.8547 (tp30) REVERT: A 526 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 588 TYR cc_start: 0.7003 (m-80) cc_final: 0.6481 (m-80) REVERT: B 24 CYS cc_start: 0.8569 (p) cc_final: 0.8307 (p) REVERT: B 526 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7898 (t80) outliers start: 27 outliers final: 14 residues processed: 83 average time/residue: 0.2269 time to fit residues: 26.4019 Evaluate side-chains 74 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 76 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9223 Z= 0.155 Angle : 0.524 9.168 12611 Z= 0.253 Chirality : 0.040 0.126 1412 Planarity : 0.004 0.038 1657 Dihedral : 6.044 64.089 1313 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.69 % Allowed : 17.89 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1146 helix: -0.49 (0.24), residues: 444 sheet: 0.89 (0.39), residues: 184 loop : -0.63 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 523 HIS 0.004 0.001 HIS B 38 PHE 0.013 0.001 PHE A 544 TYR 0.017 0.002 TYR B 472 ARG 0.003 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8581 (mm-40) REVERT: A 476 LYS cc_start: 0.7742 (mttt) cc_final: 0.7170 (mttp) REVERT: A 489 GLU cc_start: 0.8939 (tt0) cc_final: 0.8551 (tp30) REVERT: A 526 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7542 (t80) REVERT: A 588 TYR cc_start: 0.7056 (m-80) cc_final: 0.6528 (m-80) REVERT: B 24 CYS cc_start: 0.8553 (p) cc_final: 0.8260 (p) REVERT: B 526 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7988 (t80) outliers start: 25 outliers final: 16 residues processed: 84 average time/residue: 0.2257 time to fit residues: 26.6665 Evaluate side-chains 81 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 64 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9223 Z= 0.150 Angle : 0.520 8.736 12611 Z= 0.249 Chirality : 0.040 0.125 1412 Planarity : 0.004 0.037 1657 Dihedral : 5.900 64.267 1313 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.59 % Allowed : 18.10 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1146 helix: -0.19 (0.24), residues: 453 sheet: 0.98 (0.39), residues: 185 loop : -0.55 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS B 38 PHE 0.019 0.001 PHE A 570 TYR 0.017 0.002 TYR B 472 ARG 0.003 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7902 (pmm150) REVERT: A 489 GLU cc_start: 0.8871 (tt0) cc_final: 0.8480 (tp30) REVERT: A 526 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 588 TYR cc_start: 0.7144 (m-80) cc_final: 0.6616 (m-80) REVERT: B 24 CYS cc_start: 0.8534 (p) cc_final: 0.8260 (p) REVERT: B 189 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 526 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8021 (t80) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.2290 time to fit residues: 24.2643 Evaluate side-chains 80 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 67 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9223 Z= 0.160 Angle : 0.516 9.340 12611 Z= 0.249 Chirality : 0.040 0.127 1412 Planarity : 0.004 0.040 1657 Dihedral : 5.766 64.779 1313 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.48 % Allowed : 18.53 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.00 (0.25), residues: 1146 helix: 0.16 (0.24), residues: 461 sheet: 1.02 (0.39), residues: 184 loop : -0.42 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS B 38 PHE 0.014 0.001 PHE A 570 TYR 0.017 0.002 TYR B 472 ARG 0.003 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8365 (mm) cc_final: 0.8027 (mm) REVERT: A 222 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7956 (pmm150) REVERT: A 489 GLU cc_start: 0.8842 (tt0) cc_final: 0.8603 (tm-30) REVERT: A 526 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 588 TYR cc_start: 0.7131 (m-80) cc_final: 0.6875 (m-80) REVERT: B 24 CYS cc_start: 0.8531 (p) cc_final: 0.8257 (p) REVERT: B 189 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7569 (tt0) outliers start: 23 outliers final: 16 residues processed: 79 average time/residue: 0.2219 time to fit residues: 24.8230 Evaluate side-chains 77 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9223 Z= 0.201 Angle : 0.543 10.297 12611 Z= 0.260 Chirality : 0.040 0.136 1412 Planarity : 0.004 0.040 1657 Dihedral : 5.711 65.696 1311 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.80 % Allowed : 18.21 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.10 (0.25), residues: 1146 helix: 0.35 (0.24), residues: 461 sheet: 0.91 (0.39), residues: 185 loop : -0.41 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 434 HIS 0.004 0.001 HIS B 38 PHE 0.015 0.001 PHE A 544 TYR 0.016 0.002 TYR B 472 ARG 0.003 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 56 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8347 (mm) cc_final: 0.8038 (mm) REVERT: A 259 MET cc_start: 0.8438 (mmm) cc_final: 0.8217 (ttt) REVERT: A 489 GLU cc_start: 0.8828 (tt0) cc_final: 0.8611 (tm-30) REVERT: A 526 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (t80) REVERT: A 588 TYR cc_start: 0.7223 (m-80) cc_final: 0.6959 (m-80) REVERT: B 24 CYS cc_start: 0.8548 (p) cc_final: 0.8266 (p) REVERT: B 189 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7620 (tt0) outliers start: 26 outliers final: 19 residues processed: 76 average time/residue: 0.2292 time to fit residues: 24.4229 Evaluate side-chains 76 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9223 Z= 0.205 Angle : 0.559 11.083 12611 Z= 0.268 Chirality : 0.041 0.130 1412 Planarity : 0.004 0.038 1657 Dihedral : 5.739 66.078 1311 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.48 % Allowed : 18.32 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.20 (0.25), residues: 1146 helix: 0.50 (0.24), residues: 459 sheet: 0.81 (0.39), residues: 185 loop : -0.37 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 434 HIS 0.005 0.001 HIS B 38 PHE 0.014 0.001 PHE A 544 TYR 0.015 0.002 TYR B 176 ARG 0.003 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8343 (mm) cc_final: 0.8048 (mm) REVERT: A 301 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 479 TYR cc_start: 0.8197 (m-80) cc_final: 0.7795 (m-10) REVERT: A 489 GLU cc_start: 0.8842 (tt0) cc_final: 0.8618 (tm-30) REVERT: A 526 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7711 (t80) REVERT: A 588 TYR cc_start: 0.7214 (m-80) cc_final: 0.6947 (m-80) REVERT: B 24 CYS cc_start: 0.8579 (p) cc_final: 0.8296 (p) REVERT: B 189 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7677 (tt0) outliers start: 23 outliers final: 19 residues processed: 78 average time/residue: 0.2280 time to fit residues: 24.8043 Evaluate side-chains 78 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 90 optimal weight: 0.0020 chunk 9 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 96 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 overall best weight: 0.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9223 Z= 0.126 Angle : 0.534 11.755 12611 Z= 0.252 Chirality : 0.039 0.124 1412 Planarity : 0.004 0.036 1657 Dihedral : 5.446 64.619 1311 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.40 % Allowed : 19.83 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.25), residues: 1146 helix: 0.69 (0.24), residues: 461 sheet: 0.95 (0.39), residues: 186 loop : -0.26 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.003 0.001 HIS A 334 PHE 0.018 0.001 PHE A 570 TYR 0.015 0.002 TYR B 472 ARG 0.003 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8352 (mm) cc_final: 0.8055 (mm) REVERT: A 222 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7913 (pmm150) REVERT: A 479 TYR cc_start: 0.8176 (m-80) cc_final: 0.7799 (m-10) REVERT: A 489 GLU cc_start: 0.8813 (tt0) cc_final: 0.8581 (tm-30) REVERT: B 24 CYS cc_start: 0.8529 (p) cc_final: 0.8283 (p) REVERT: B 189 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: B 222 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (pmm150) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.2424 time to fit residues: 22.6061 Evaluate side-chains 66 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.123231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.095127 restraints weight = 20711.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.096843 restraints weight = 13193.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097244 restraints weight = 10860.055| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9223 Z= 0.133 Angle : 0.533 11.980 12611 Z= 0.249 Chirality : 0.039 0.123 1412 Planarity : 0.004 0.034 1657 Dihedral : 5.202 64.510 1309 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.29 % Allowed : 19.94 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.61 (0.25), residues: 1146 helix: 0.90 (0.24), residues: 459 sheet: 1.08 (0.38), residues: 186 loop : -0.23 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 523 HIS 0.003 0.000 HIS A 334 PHE 0.019 0.001 PHE A 570 TYR 0.016 0.002 TYR B 472 ARG 0.003 0.000 ARG B 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.02 seconds wall clock time: 35 minutes 48.52 seconds (2148.52 seconds total)