Starting phenix.real_space_refine on Thu Mar 14 15:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj8_12939/03_2024/7oj8_12939_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 59 5.16 5 C 5958 2.51 5 N 1484 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'ATP': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'ATP': 1, 'CLR': 2, 'FY5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.61, per 1000 atoms: 0.61 Number of scatterers: 9148 At special positions: 0 Unit cell: (78.66, 90.896, 129.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 6 15.00 O 1641 8.00 N 1484 7.00 C 5958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 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: 4.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 56.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.756A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.607A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.059A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.212A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.569A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 422 through 460 removed outlier: 4.506A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS A 452 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 485 - end of helix removed outlier: 4.785A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 527 Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.949A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 3.529A pdb=" N SER A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP A 567 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.560A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 624 through 649 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.757A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.608A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.059A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.214A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.569A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 422 through 460 removed outlier: 4.506A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 485 - end of helix removed outlier: 4.785A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 527 Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.949A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 removed outlier: 3.528A pdb=" N SER B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP B 567 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.560A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 598 No H-bonds generated for 'chain 'B' and resid 595 through 598' Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 624 through 649 Processing sheet with id= A, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= B, first strand: chain 'A' and resid 74 through 78 removed outlier: 3.523A pdb=" N ILE A 238 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 122 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 255 through 260 removed outlier: 3.679A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= E, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.522A pdb=" N ILE B 238 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 122 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 255 through 260 removed outlier: 3.679A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1413 1.31 - 1.44: 2494 1.44 - 1.57: 5327 1.57 - 1.70: 27 1.70 - 1.83: 94 Bond restraints: 9355 Sorted by residual: bond pdb=" C5 ATP B1501 " pdb=" N7 ATP B1501 " ideal model delta sigma weight residual 1.387 1.521 -0.134 1.00e-02 1.00e+04 1.79e+02 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.76e+02 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.265 0.109 1.00e-02 1.00e+04 1.18e+02 bond pdb=" C4 ATP B1501 " pdb=" N9 ATP B1501 " ideal model delta sigma weight residual 1.374 1.266 0.108 1.00e-02 1.00e+04 1.16e+02 bond pdb=" C6 ATP A1501 " pdb=" N6 ATP A1501 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.10e+02 ... (remaining 9350 not shown) Histogram of bond angle deviations from ideal: 97.66 - 106.01: 233 106.01 - 114.36: 5725 114.36 - 122.70: 6176 122.70 - 131.05: 539 131.05 - 139.40: 30 Bond angle restraints: 12703 Sorted by residual: angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 116.58 23.29 1.00e+00 1.00e+00 5.43e+02 angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 118.24 18.59 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.28 18.55 1.00e+00 1.00e+00 3.44e+02 angle pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " pdb=" C8 ATP A1501 " ideal model delta sigma weight residual 105.72 121.87 -16.15 1.00e+00 1.00e+00 2.61e+02 ... (remaining 12698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5340 17.88 - 35.77: 361 35.77 - 53.65: 69 53.65 - 71.53: 12 71.53 - 89.42: 14 Dihedral angle restraints: 5796 sinusoidal: 2482 harmonic: 3314 Sorted by residual: dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.87 53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.85 53.85 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LEU A 64 " pdb=" C LEU A 64 " pdb=" N SER A 65 " pdb=" CA SER A 65 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1253 0.073 - 0.147: 187 0.147 - 0.220: 24 0.220 - 0.294: 10 0.294 - 0.367: 4 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C17 CLR B1503 " pdb=" C13 CLR B1503 " pdb=" C16 CLR B1503 " pdb=" C20 CLR B1503 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 CLR A1503 " pdb=" C13 CLR A1503 " pdb=" C16 CLR A1503 " pdb=" C20 CLR A1503 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C17 CLR B1504 " pdb=" C13 CLR B1504 " pdb=" C16 CLR B1504 " pdb=" C20 CLR B1504 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1475 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 65 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C SER B 65 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 65 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 65 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C SER A 65 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 65 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 98 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 99 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 155 2.67 - 3.23: 9454 3.23 - 3.79: 13824 3.79 - 4.34: 18393 4.34 - 4.90: 30491 Nonbonded interactions: 72317 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.114 2.440 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.249 2.440 nonbonded pdb=" OE1 GLN A 393 " pdb=" OG SER B 535 " model vdw 2.395 2.440 ... (remaining 72312 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' and (resid 34 through 654 or resid 1501 or resid 1503)) selection = (chain 'B' and (resid 34 through 654 or resid 1501 or resid 1503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.030 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 29.950 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.010 0.190 9355 Z= 0.675 Angle : 1.145 23.292 12703 Z= 0.731 Chirality : 0.059 0.367 1478 Planarity : 0.004 0.046 1544 Dihedral : 13.090 89.418 3659 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.29 % Favored : 94.18 % Rotamer: Outliers : 0.41 % Allowed : 4.38 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1134 helix: 0.23 (0.19), residues: 672 sheet: -1.55 (0.49), residues: 98 loop : -2.24 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 624 HIS 0.004 0.001 HIS A 283 PHE 0.017 0.002 PHE B 507 TYR 0.016 0.002 TYR B 342 ARG 0.004 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8462 (mttt) cc_final: 0.8236 (mttp) REVERT: A 263 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7325 (mmt90) REVERT: A 265 MET cc_start: 0.7120 (mmt) cc_final: 0.6722 (mmp) REVERT: A 521 SER cc_start: 0.9032 (m) cc_final: 0.8795 (p) REVERT: A 523 MET cc_start: 0.8433 (ttp) cc_final: 0.7930 (ttt) REVERT: B 483 MET cc_start: 0.8109 (tmm) cc_final: 0.7846 (ttm) REVERT: B 514 MET cc_start: 0.8531 (mtt) cc_final: 0.8330 (mtm) outliers start: 4 outliers final: 0 residues processed: 265 average time/residue: 0.2283 time to fit residues: 81.2148 Evaluate side-chains 144 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 166 GLN B 222 ASN B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9355 Z= 0.214 Angle : 0.642 15.051 12703 Z= 0.324 Chirality : 0.043 0.384 1478 Planarity : 0.004 0.058 1544 Dihedral : 8.636 72.477 1595 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 3.77 % Allowed : 11.30 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1134 helix: 1.13 (0.20), residues: 676 sheet: -0.10 (0.63), residues: 62 loop : -1.68 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 564 HIS 0.012 0.001 HIS B 457 PHE 0.017 0.001 PHE B 39 TYR 0.020 0.002 TYR A 413 ARG 0.011 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8433 (mttt) cc_final: 0.8213 (mttp) REVERT: A 207 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 222 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: A 242 ILE cc_start: 0.8534 (tp) cc_final: 0.8192 (pt) REVERT: A 243 HIS cc_start: 0.7611 (t70) cc_final: 0.7270 (t-90) REVERT: A 263 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7506 (mmt90) REVERT: A 265 MET cc_start: 0.7149 (mmt) cc_final: 0.6805 (mmp) REVERT: A 343 LYS cc_start: 0.7938 (mptt) cc_final: 0.7633 (mppt) REVERT: A 393 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8018 (pt0) REVERT: A 521 SER cc_start: 0.8913 (m) cc_final: 0.8639 (p) REVERT: B 71 MET cc_start: 0.7047 (mmt) cc_final: 0.6636 (mmt) REVERT: B 187 SER cc_start: 0.7834 (m) cc_final: 0.7617 (p) REVERT: B 190 GLU cc_start: 0.7323 (mp0) cc_final: 0.6794 (mp0) outliers start: 37 outliers final: 19 residues processed: 195 average time/residue: 0.2006 time to fit residues: 54.8758 Evaluate side-chains 161 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 28 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 222 ASN B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9355 Z= 0.214 Angle : 0.588 13.137 12703 Z= 0.300 Chirality : 0.042 0.224 1478 Planarity : 0.003 0.038 1544 Dihedral : 7.983 79.188 1595 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.48 % Allowed : 13.65 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1134 helix: 1.44 (0.20), residues: 672 sheet: -0.06 (0.56), residues: 62 loop : -1.61 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.010 0.001 HIS B 457 PHE 0.014 0.001 PHE A 277 TYR 0.020 0.001 TYR A 413 ARG 0.008 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8440 (mttt) cc_final: 0.8222 (mttp) REVERT: A 207 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8357 (mt) REVERT: A 222 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m-40) REVERT: A 243 HIS cc_start: 0.7736 (t70) cc_final: 0.7513 (t-90) REVERT: A 263 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7653 (mmt90) REVERT: A 265 MET cc_start: 0.7160 (mmt) cc_final: 0.6838 (mmp) REVERT: A 296 ASP cc_start: 0.7291 (m-30) cc_final: 0.6983 (m-30) REVERT: A 343 LYS cc_start: 0.7961 (mptt) cc_final: 0.7713 (mppt) REVERT: B 71 MET cc_start: 0.6965 (mmt) cc_final: 0.6593 (mmt) REVERT: B 187 SER cc_start: 0.7941 (m) cc_final: 0.7727 (p) REVERT: B 190 GLU cc_start: 0.7357 (mp0) cc_final: 0.6785 (mp0) REVERT: B 246 ARG cc_start: 0.7374 (mtp-110) cc_final: 0.6985 (mtp-110) outliers start: 44 outliers final: 31 residues processed: 183 average time/residue: 0.1904 time to fit residues: 49.7296 Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 622 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 244 GLN B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9355 Z= 0.259 Angle : 0.605 16.452 12703 Z= 0.311 Chirality : 0.042 0.192 1478 Planarity : 0.004 0.042 1544 Dihedral : 7.518 85.434 1595 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.38 % Allowed : 14.77 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1134 helix: 1.38 (0.20), residues: 672 sheet: -0.11 (0.55), residues: 68 loop : -1.63 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.004 0.001 HIS B 243 PHE 0.014 0.001 PHE A 277 TYR 0.018 0.001 TYR A 413 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7084 (ptmm) REVERT: A 97 LYS cc_start: 0.8477 (mttt) cc_final: 0.8220 (mttp) REVERT: A 207 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 222 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7576 (m-40) REVERT: A 243 HIS cc_start: 0.7739 (t70) cc_final: 0.7467 (t-90) REVERT: A 263 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7643 (mmt90) REVERT: A 265 MET cc_start: 0.7087 (mmt) cc_final: 0.6761 (mmp) REVERT: A 296 ASP cc_start: 0.7346 (m-30) cc_final: 0.7055 (m-30) REVERT: A 343 LYS cc_start: 0.8014 (mptt) cc_final: 0.7780 (mppt) REVERT: B 190 GLU cc_start: 0.7398 (mp0) cc_final: 0.7011 (mp0) REVERT: B 385 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6142 (t80) outliers start: 43 outliers final: 33 residues processed: 169 average time/residue: 0.1920 time to fit residues: 46.2882 Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 622 SER 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: 5.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 166 GLN B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 9355 Z= 0.505 Angle : 0.786 14.864 12703 Z= 0.408 Chirality : 0.048 0.154 1478 Planarity : 0.005 0.046 1544 Dihedral : 7.579 85.121 1595 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.70 % Allowed : 15.17 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1134 helix: 0.88 (0.20), residues: 654 sheet: -0.77 (0.54), residues: 88 loop : -1.46 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 379 HIS 0.005 0.001 HIS B 267 PHE 0.023 0.002 PHE B 495 TYR 0.026 0.002 TYR B 413 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 130 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7167 (ptmm) REVERT: A 222 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7789 (m-40) REVERT: A 243 HIS cc_start: 0.7749 (t70) cc_final: 0.7516 (t-90) REVERT: A 263 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7315 (mpp-170) REVERT: A 296 ASP cc_start: 0.7402 (m-30) cc_final: 0.7057 (m-30) REVERT: A 515 MET cc_start: 0.8818 (mmm) cc_final: 0.8538 (mmm) REVERT: B 71 MET cc_start: 0.7381 (mmt) cc_final: 0.7137 (mmt) REVERT: B 172 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8053 (mmtm) REVERT: B 385 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6656 (t80) outliers start: 56 outliers final: 42 residues processed: 170 average time/residue: 0.1956 time to fit residues: 47.2275 Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 601 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9355 Z= 0.179 Angle : 0.594 16.287 12703 Z= 0.301 Chirality : 0.040 0.159 1478 Planarity : 0.004 0.035 1544 Dihedral : 6.608 75.142 1595 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.48 % Allowed : 16.80 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1134 helix: 1.40 (0.20), residues: 666 sheet: -0.12 (0.59), residues: 68 loop : -1.52 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.014 0.001 HIS A 155 PHE 0.016 0.001 PHE B 39 TYR 0.016 0.001 TYR B 342 ARG 0.011 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7149 (ptmm) REVERT: A 207 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 243 HIS cc_start: 0.7672 (t70) cc_final: 0.7446 (t-90) REVERT: A 263 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7744 (mmt90) REVERT: A 343 LYS cc_start: 0.8066 (mptt) cc_final: 0.7848 (mppt) REVERT: B 71 MET cc_start: 0.7192 (mmt) cc_final: 0.6860 (mmt) REVERT: B 172 LYS cc_start: 0.8273 (mtmm) cc_final: 0.8065 (mmtm) REVERT: B 296 ASP cc_start: 0.6720 (p0) cc_final: 0.6398 (p0) REVERT: B 385 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6489 (t80) outliers start: 44 outliers final: 31 residues processed: 169 average time/residue: 0.1992 time to fit residues: 47.9512 Evaluate side-chains 161 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 622 SER 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: 0.7980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 222 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 557 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9355 Z= 0.229 Angle : 0.605 14.722 12703 Z= 0.308 Chirality : 0.041 0.151 1478 Planarity : 0.004 0.040 1544 Dihedral : 6.329 68.041 1595 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.48 % Allowed : 17.82 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1134 helix: 1.36 (0.20), residues: 668 sheet: -0.03 (0.59), residues: 68 loop : -1.52 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS B 267 PHE 0.020 0.001 PHE A 277 TYR 0.014 0.001 TYR B 342 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7121 (ptmm) REVERT: A 207 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 243 HIS cc_start: 0.7667 (t70) cc_final: 0.7440 (t-90) REVERT: A 263 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7770 (mmt90) REVERT: A 515 MET cc_start: 0.8759 (mmm) cc_final: 0.8439 (mmm) REVERT: B 71 MET cc_start: 0.7152 (mmt) cc_final: 0.6860 (mmt) REVERT: B 172 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8046 (mmtm) REVERT: B 385 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6569 (t80) outliers start: 44 outliers final: 35 residues processed: 164 average time/residue: 0.1867 time to fit residues: 44.0569 Evaluate side-chains 161 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9355 Z= 0.213 Angle : 0.593 14.065 12703 Z= 0.300 Chirality : 0.040 0.153 1478 Planarity : 0.004 0.040 1544 Dihedral : 6.112 62.723 1595 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.87 % Allowed : 18.33 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1134 helix: 1.46 (0.20), residues: 666 sheet: 0.07 (0.58), residues: 68 loop : -1.48 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.003 0.001 HIS B 267 PHE 0.025 0.001 PHE A 277 TYR 0.013 0.001 TYR A 413 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 243 HIS cc_start: 0.7668 (t70) cc_final: 0.7455 (t-90) REVERT: A 263 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7780 (mmt90) REVERT: A 515 MET cc_start: 0.8709 (mmm) cc_final: 0.8416 (mmm) REVERT: B 71 MET cc_start: 0.7114 (mmt) cc_final: 0.6819 (mmt) REVERT: B 172 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8059 (mmtm) REVERT: B 385 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6622 (t80) REVERT: B 511 PHE cc_start: 0.7945 (t80) cc_final: 0.6844 (m-10) REVERT: B 515 MET cc_start: 0.8318 (mmm) cc_final: 0.7855 (mpp) outliers start: 38 outliers final: 30 residues processed: 155 average time/residue: 0.1963 time to fit residues: 43.2796 Evaluate side-chains 155 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL 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: 6.9990 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 222 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9355 Z= 0.361 Angle : 0.677 13.329 12703 Z= 0.347 Chirality : 0.043 0.152 1478 Planarity : 0.004 0.045 1544 Dihedral : 6.274 60.790 1595 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.77 % Allowed : 18.84 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1134 helix: 1.39 (0.20), residues: 648 sheet: -0.20 (0.54), residues: 88 loop : -1.23 (0.35), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.029 0.002 PHE A 277 TYR 0.018 0.002 TYR B 413 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7150 (ptmm) REVERT: A 207 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (mt) REVERT: A 243 HIS cc_start: 0.7772 (t70) cc_final: 0.7535 (t-90) REVERT: A 263 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7776 (mmt90) REVERT: A 515 MET cc_start: 0.8769 (mmm) cc_final: 0.8464 (mmm) REVERT: B 71 MET cc_start: 0.7209 (mmt) cc_final: 0.6916 (mmt) REVERT: B 172 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8059 (mmtm) REVERT: B 385 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6705 (t80) outliers start: 37 outliers final: 32 residues processed: 148 average time/residue: 0.2030 time to fit residues: 42.5702 Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 222 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9355 Z= 0.271 Angle : 0.651 13.205 12703 Z= 0.330 Chirality : 0.041 0.157 1478 Planarity : 0.004 0.075 1544 Dihedral : 6.151 58.036 1595 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.36 % Allowed : 19.65 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1134 helix: 1.46 (0.20), residues: 648 sheet: 0.10 (0.60), residues: 68 loop : -1.26 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS B 267 PHE 0.029 0.002 PHE A 277 TYR 0.015 0.002 TYR B 413 ARG 0.006 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7161 (ptmm) REVERT: A 207 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (mt) REVERT: A 243 HIS cc_start: 0.7760 (t70) cc_final: 0.7531 (t-90) REVERT: A 263 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7774 (mmt90) REVERT: A 515 MET cc_start: 0.8742 (mmm) cc_final: 0.8439 (mmm) REVERT: B 71 MET cc_start: 0.7146 (mmt) cc_final: 0.6885 (mmt) REVERT: B 172 LYS cc_start: 0.8273 (mtmm) cc_final: 0.8065 (mmtm) REVERT: B 385 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6729 (t80) outliers start: 33 outliers final: 29 residues processed: 152 average time/residue: 0.1984 time to fit residues: 43.0351 Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 222 ASN B 244 GLN B 299 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102934 restraints weight = 17325.499| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.98 r_work: 0.3316 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9355 Z= 0.183 Angle : 0.603 12.188 12703 Z= 0.302 Chirality : 0.039 0.156 1478 Planarity : 0.004 0.051 1544 Dihedral : 5.754 51.109 1595 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.36 % Allowed : 19.86 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1134 helix: 1.73 (0.21), residues: 648 sheet: 0.30 (0.58), residues: 68 loop : -1.27 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 PHE 0.021 0.001 PHE B 448 TYR 0.011 0.001 TYR B 463 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.16 seconds wall clock time: 36 minutes 47.54 seconds (2207.54 seconds total)