Starting phenix.real_space_refine on Mon Mar 25 10:39:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/03_2024/6tfj_10492.pdb" } resolution = 2.9 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= 0.005 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 S 64 5.16 5 C 15374 2.51 5 N 3938 2.21 5 O 4866 1.98 5 H 24098 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ARG 501": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 761": "OE1" <-> "OE2" Residue "B ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 761": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C ARG 501": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 761": "OE1" <-> "OE2" Residue "D ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 761": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 12080 Classifications: {'peptide': 764} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 746} Chain breaks: 1 Chain: "B" Number of atoms: 12090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 12090 Classifications: {'peptide': 765} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 746} Chain breaks: 1 Chain: "C" Number of atoms: 12080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 12080 Classifications: {'peptide': 764} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 746} Chain breaks: 1 Chain: "D" Number of atoms: 12090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 12090 Classifications: {'peptide': 765} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 746} Chain breaks: 1 Time building chain proxies: 20.31, per 1000 atoms: 0.42 Number of scatterers: 48340 At special positions: 0 Unit cell: (151.96, 149.864, 185.496, 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 64 16.00 O 4866 8.00 N 3938 7.00 C 15374 6.00 H 24098 1.00 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: 38.08 Conformation dependent library (CDL) restraints added in 5.0 seconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5732 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 40 sheets defined 31.7% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 48 through 78 Processing helix chain 'A' and resid 83 through 151 Proline residue: A 119 - end of helix removed outlier: 3.644A pdb=" N GLN A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 137 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLN A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 190 Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 208 through 219 removed outlier: 5.420A pdb=" N LEU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 267 through 296 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 54 through 78 removed outlier: 4.041A pdb=" N GLY B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 116 Processing helix chain 'B' and resid 118 through 152 removed outlier: 4.863A pdb=" N ALA B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 189 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 203 through 219 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 267 through 296 Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 48 through 78 Processing helix chain 'C' and resid 83 through 151 Proline residue: C 119 - end of helix removed outlier: 3.622A pdb=" N GLN C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 190 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 208 through 219 removed outlier: 5.493A pdb=" N LEU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 267 through 296 Processing helix chain 'C' and resid 303 through 321 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 511 through 517 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 54 through 78 removed outlier: 3.998A pdb=" N GLY D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 116 Processing helix chain 'D' and resid 118 through 152 removed outlier: 4.847A pdb=" N ALA D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 135 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 189 Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 267 through 296 Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 511 through 517 Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.546A pdb=" N GLY A 491 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 492 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.553A pdb=" N ASN A 334 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.945A pdb=" N THR A 439 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 425 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU A 437 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 427 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 435 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN A 453 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 479 through 482 removed outlier: 5.707A pdb=" N LEU A 357 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 375 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 359 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 407 through 409 Processing sheet with id= F, first strand: chain 'A' and resid 573 through 575 Processing sheet with id= G, first strand: chain 'A' and resid 581 through 584 removed outlier: 4.137A pdb=" N TYR A 619 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP A 611 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE A 617 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 596 through 598 Processing sheet with id= I, first strand: chain 'A' and resid 685 through 687 Processing sheet with id= J, first strand: chain 'A' and resid 690 through 693 Processing sheet with id= K, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.727A pdb=" N GLY B 491 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 492 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 334 through 338 Processing sheet with id= M, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.800A pdb=" N THR B 439 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 425 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B 437 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE B 427 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG B 435 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN B 453 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 479 through 482 removed outlier: 5.526A pdb=" N LEU B 357 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 375 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 359 " --> pdb=" O TYR B 373 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 407 through 409 Processing sheet with id= P, first strand: chain 'B' and resid 573 through 575 Processing sheet with id= Q, first strand: chain 'B' and resid 581 through 584 removed outlier: 4.134A pdb=" N TYR B 619 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ASP B 611 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 617 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 596 through 598 Processing sheet with id= S, first strand: chain 'B' and resid 685 through 687 Processing sheet with id= T, first strand: chain 'B' and resid 690 through 693 Processing sheet with id= U, first strand: chain 'C' and resid 329 through 331 removed outlier: 4.073A pdb=" N GLY C 491 " --> pdb=" O LYS C 508 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 492 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 334 through 338 removed outlier: 3.625A pdb=" N ASN C 334 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.982A pdb=" N THR C 439 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE C 425 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU C 437 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE C 427 " --> pdb=" O ARG C 435 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG C 435 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN C 453 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 479 through 482 removed outlier: 5.635A pdb=" N LEU C 357 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 375 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 359 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= Z, first strand: chain 'C' and resid 573 through 575 Processing sheet with id= AA, first strand: chain 'C' and resid 581 through 584 removed outlier: 4.114A pdb=" N TYR C 619 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ASP C 611 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 617 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 596 through 598 Processing sheet with id= AC, first strand: chain 'C' and resid 685 through 687 Processing sheet with id= AD, first strand: chain 'C' and resid 690 through 693 Processing sheet with id= AE, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.784A pdb=" N GLY D 491 " --> pdb=" O LYS D 508 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 492 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 414 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 334 through 338 Processing sheet with id= AG, first strand: chain 'D' and resid 346 through 350 removed outlier: 6.719A pdb=" N THR D 439 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE D 425 " --> pdb=" O GLU D 437 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU D 437 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 427 " --> pdb=" O ARG D 435 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG D 435 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASN D 453 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 479 through 482 removed outlier: 5.546A pdb=" N LEU D 357 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA D 375 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 359 " --> pdb=" O TYR D 373 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'D' and resid 573 through 575 Processing sheet with id= AK, first strand: chain 'D' and resid 581 through 584 removed outlier: 4.143A pdb=" N TYR D 619 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ASP D 611 " --> pdb=" O ILE D 617 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE D 617 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 596 through 598 Processing sheet with id= AM, first strand: chain 'D' and resid 685 through 687 Processing sheet with id= AN, first strand: chain 'D' and resid 690 through 693 1209 hydrogen bonds defined for protein. 3393 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: 23.28 Time building geometry restraints manager: 39.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24086 1.03 - 1.22: 12 1.22 - 1.42: 10115 1.42 - 1.61: 14405 1.61 - 1.81: 116 Bond restraints: 48734 Sorted by residual: bond pdb=" C MET A 476 " pdb=" N PRO A 477 " ideal model delta sigma weight residual 1.332 1.344 -0.013 1.26e-02 6.30e+03 1.02e+00 bond pdb=" C MET C 476 " pdb=" N PRO C 477 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.26e-02 6.30e+03 9.66e-01 bond pdb=" CA LYS B 152 " pdb=" C LYS B 152 " ideal model delta sigma weight residual 1.523 1.540 -0.016 1.80e-02 3.09e+03 8.25e-01 bond pdb=" CA ILE B 481 " pdb=" CB ILE B 481 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 7.75e-01 bond pdb=" CA ILE D 481 " pdb=" CB ILE D 481 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 7.15e-01 ... (remaining 48729 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.69: 421 106.69 - 113.55: 59047 113.55 - 120.41: 15388 120.41 - 127.26: 13187 127.26 - 134.12: 125 Bond angle restraints: 88168 Sorted by residual: angle pdb=" N ILE B 358 " pdb=" CA ILE B 358 " pdb=" C ILE B 358 " ideal model delta sigma weight residual 113.47 110.76 2.71 1.01e+00 9.80e-01 7.19e+00 angle pdb=" N ILE D 358 " pdb=" CA ILE D 358 " pdb=" C ILE D 358 " ideal model delta sigma weight residual 113.47 110.92 2.55 1.01e+00 9.80e-01 6.39e+00 angle pdb=" C ASN B 321 " pdb=" N ILE B 322 " pdb=" CA ILE B 322 " ideal model delta sigma weight residual 123.16 121.13 2.03 1.06e+00 8.90e-01 3.67e+00 angle pdb=" N ILE C 481 " pdb=" CA ILE C 481 " pdb=" C ILE C 481 " ideal model delta sigma weight residual 109.34 105.77 3.57 2.08e+00 2.31e-01 2.95e+00 angle pdb=" CA ILE B 358 " pdb=" C ILE B 358 " pdb=" O ILE B 358 " ideal model delta sigma weight residual 118.98 120.49 -1.51 9.00e-01 1.23e+00 2.81e+00 ... (remaining 88163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 21559 16.88 - 33.76: 902 33.76 - 50.64: 257 50.64 - 67.52: 137 67.52 - 84.40: 9 Dihedral angle restraints: 22864 sinusoidal: 12554 harmonic: 10310 Sorted by residual: dihedral pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" N GLU A 406 " pdb=" CA GLU A 406 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " pdb=" CD GLU A 181 " pdb=" OE1 GLU A 181 " ideal model delta sinusoidal sigma weight residual 0.00 -84.40 84.40 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" CA LYS C 762 " pdb=" CB LYS C 762 " pdb=" CG LYS C 762 " pdb=" CD LYS C 762 " ideal model delta sinusoidal sigma weight residual -60.00 -119.48 59.48 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 22861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2500 0.029 - 0.058: 899 0.058 - 0.087: 213 0.087 - 0.116: 166 0.116 - 0.145: 68 Chirality restraints: 3846 Sorted by residual: chirality pdb=" CA ILE B 733 " pdb=" N ILE B 733 " pdb=" C ILE B 733 " pdb=" CB ILE B 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE A 733 " pdb=" N ILE A 733 " pdb=" C ILE A 733 " pdb=" CB ILE A 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE D 733 " pdb=" N ILE D 733 " pdb=" C ILE D 733 " pdb=" CB ILE D 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 3843 not shown) Planarity restraints: 7270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 675 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 676 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 675 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 676 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 676 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 676 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 675 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 676 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " 0.015 5.00e-02 4.00e+02 ... (remaining 7267 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 953 2.11 - 2.73: 88528 2.73 - 3.35: 139324 3.35 - 3.98: 177266 3.98 - 4.60: 284063 Nonbonded interactions: 690134 Sorted by model distance: nonbonded pdb=" HH TYR B 272 " pdb=" OD2 ASP B 519 " model vdw 1.484 1.850 nonbonded pdb=" HH TYR D 272 " pdb=" OD2 ASP D 519 " model vdw 1.484 1.850 nonbonded pdb=" OH TYR C 599 " pdb=" HH TYR C 619 " model vdw 1.584 1.850 nonbonded pdb="HH22 ARG B 246 " pdb=" OE1 GLU B 254 " model vdw 1.596 1.850 nonbonded pdb=" H LYS D 592 " pdb=" O THR D 638 " model vdw 1.602 1.850 ... (remaining 690129 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 14 through 190 or resid 204 through 789)) selection = (chain 'B' and (resid 14 through 190 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 205 through 789)) selection = (chain 'C' and (resid 14 through 190 or resid 204 through 789)) selection = (chain 'D' and (resid 14 through 190 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 205 through 789)) } 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: 0.920 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: 0.700 Extract box with map and model: 6.620 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 151.340 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.002 0.025 24636 Z= 0.131 Angle : 0.426 4.562 33336 Z= 0.242 Chirality : 0.039 0.145 3846 Planarity : 0.002 0.031 4288 Dihedral : 9.890 84.396 9170 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % 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: -2.53 (0.14), residues: 3042 helix: 0.20 (0.15), residues: 1014 sheet: -1.75 (0.17), residues: 770 loop : -3.25 (0.14), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 658 HIS 0.004 0.001 HIS A 235 PHE 0.016 0.001 PHE A 26 TYR 0.011 0.001 TYR A 510 ARG 0.002 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8132 (mmt) cc_final: 0.7567 (mmt) REVERT: A 396 MET cc_start: 0.7184 (mmm) cc_final: 0.6761 (mmp) REVERT: A 495 GLN cc_start: 0.6664 (mm-40) cc_final: 0.6430 (tp40) REVERT: A 728 ASP cc_start: 0.5509 (t0) cc_final: 0.5258 (m-30) REVERT: B 50 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6847 (mm-30) REVERT: B 223 ASP cc_start: 0.7655 (p0) cc_final: 0.7452 (p0) REVERT: B 431 MET cc_start: 0.7346 (mmm) cc_final: 0.6981 (mmt) REVERT: B 551 PRO cc_start: 0.7062 (Cg_exo) cc_final: 0.6240 (Cg_endo) REVERT: C 396 MET cc_start: 0.6808 (mmm) cc_final: 0.6413 (mmp) REVERT: C 411 THR cc_start: 0.6065 (p) cc_final: 0.5736 (p) REVERT: C 495 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6390 (tp40) REVERT: C 539 VAL cc_start: 0.7868 (t) cc_final: 0.7576 (m) REVERT: D 50 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 223 ASP cc_start: 0.7664 (p0) cc_final: 0.7462 (p0) REVERT: D 431 MET cc_start: 0.7137 (mmm) cc_final: 0.6867 (mmt) REVERT: D 551 PRO cc_start: 0.6842 (Cg_exo) cc_final: 0.6559 (Cg_endo) REVERT: D 684 TRP cc_start: 0.5518 (m100) cc_final: 0.5259 (m100) outliers start: 3 outliers final: 5 residues processed: 477 average time/residue: 2.3516 time to fit residues: 1335.4674 Evaluate side-chains 282 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain D residue 633 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 238 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN B 499 ASN D 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24636 Z= 0.223 Angle : 0.504 4.805 33336 Z= 0.271 Chirality : 0.041 0.149 3846 Planarity : 0.003 0.049 4288 Dihedral : 4.519 79.669 3276 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 1.49 % Allowed : 10.97 % Favored : 87.54 % 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: -1.72 (0.14), residues: 3042 helix: 1.06 (0.15), residues: 1018 sheet: -1.39 (0.17), residues: 792 loop : -2.92 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 658 HIS 0.004 0.001 HIS C 355 PHE 0.020 0.002 PHE A 26 TYR 0.014 0.001 TYR A 510 ARG 0.005 0.001 ARG C 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7405 (mmm) cc_final: 0.6944 (mmp) REVERT: B 50 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6923 (mm-30) REVERT: B 432 LYS cc_start: 0.7210 (ttmt) cc_final: 0.6993 (tppt) REVERT: B 684 TRP cc_start: 0.5587 (m100) cc_final: 0.5325 (m100) REVERT: C 129 MET cc_start: 0.7463 (tpp) cc_final: 0.7190 (mmp) REVERT: C 396 MET cc_start: 0.6981 (mmm) cc_final: 0.6587 (mmp) REVERT: C 539 VAL cc_start: 0.7828 (t) cc_final: 0.7599 (m) REVERT: D 431 MET cc_start: 0.7161 (mmm) cc_final: 0.6796 (mmt) outliers start: 41 outliers final: 16 residues processed: 326 average time/residue: 2.1850 time to fit residues: 875.9863 Evaluate side-chains 277 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 633 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24636 Z= 0.315 Angle : 0.566 5.634 33336 Z= 0.308 Chirality : 0.043 0.144 3846 Planarity : 0.004 0.046 4288 Dihedral : 4.804 42.383 3270 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 2.59 % Allowed : 12.46 % Favored : 84.95 % 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: -1.62 (0.14), residues: 3042 helix: 1.00 (0.15), residues: 1020 sheet: -1.22 (0.17), residues: 828 loop : -2.86 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 658 HIS 0.009 0.001 HIS A 355 PHE 0.029 0.002 PHE C 26 TYR 0.019 0.002 TYR A 510 ARG 0.005 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 281 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.6860 (p0) cc_final: 0.6605 (p0) REVERT: A 238 MET cc_start: 0.8102 (mmt) cc_final: 0.7895 (mmt) REVERT: A 396 MET cc_start: 0.7599 (mmm) cc_final: 0.7209 (mmp) REVERT: A 413 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7591 (m110) REVERT: B 49 ASP cc_start: 0.6540 (p0) cc_final: 0.6258 (p0) REVERT: B 259 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: C 108 ASP cc_start: 0.6907 (p0) cc_final: 0.6636 (p0) REVERT: C 129 MET cc_start: 0.7547 (tpp) cc_final: 0.7337 (mmp) REVERT: C 147 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6731 (tt0) REVERT: C 238 MET cc_start: 0.8024 (mmt) cc_final: 0.7350 (mmt) REVERT: C 396 MET cc_start: 0.7187 (mmm) cc_final: 0.6773 (mmp) REVERT: C 540 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: D 69 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7655 (t0) REVERT: D 259 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: D 431 MET cc_start: 0.7163 (mmm) cc_final: 0.6722 (mmt) REVERT: D 540 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7739 (tm-30) outliers start: 71 outliers final: 28 residues processed: 324 average time/residue: 2.1122 time to fit residues: 830.5703 Evaluate side-chains 288 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 0.2980 chunk 145 optimal weight: 0.0980 chunk 263 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 282 GLN D 56 GLN D 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24636 Z= 0.137 Angle : 0.463 5.000 33336 Z= 0.250 Chirality : 0.040 0.144 3846 Planarity : 0.003 0.047 4288 Dihedral : 4.380 44.070 3270 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 1.71 % Allowed : 14.72 % Favored : 83.56 % 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: -1.07 (0.15), residues: 3042 helix: 1.69 (0.16), residues: 1020 sheet: -0.97 (0.18), residues: 794 loop : -2.68 (0.15), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 658 HIS 0.004 0.001 HIS C 235 PHE 0.021 0.001 PHE D 636 TYR 0.012 0.001 TYR B 599 ARG 0.005 0.000 ARG C 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7587 (mmm) cc_final: 0.7105 (mmp) REVERT: B 49 ASP cc_start: 0.6477 (p0) cc_final: 0.6244 (p0) REVERT: B 658 TRP cc_start: 0.4135 (p90) cc_final: 0.3702 (p90) REVERT: C 34 MET cc_start: 0.6939 (mtt) cc_final: 0.6599 (mtt) REVERT: C 108 ASP cc_start: 0.6895 (p0) cc_final: 0.6633 (p0) REVERT: C 147 GLN cc_start: 0.6902 (mt0) cc_final: 0.6657 (tt0) REVERT: C 396 MET cc_start: 0.7107 (mmm) cc_final: 0.6687 (mmp) REVERT: D 431 MET cc_start: 0.7071 (mmm) cc_final: 0.6706 (mmt) outliers start: 47 outliers final: 16 residues processed: 289 average time/residue: 2.0943 time to fit residues: 742.8132 Evaluate side-chains 259 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 633 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 GLN D 56 GLN D 69 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24636 Z= 0.308 Angle : 0.539 7.070 33336 Z= 0.294 Chirality : 0.042 0.157 3846 Planarity : 0.004 0.046 4288 Dihedral : 4.728 46.498 3270 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 2.22 % Allowed : 15.23 % Favored : 82.54 % 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: -1.24 (0.15), residues: 3042 helix: 1.37 (0.16), residues: 1022 sheet: -0.95 (0.18), residues: 832 loop : -2.75 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 658 HIS 0.008 0.001 HIS A 355 PHE 0.026 0.002 PHE C 26 TYR 0.018 0.002 TYR A 510 ARG 0.005 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 250 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6703 (mttp) REVERT: A 238 MET cc_start: 0.7890 (mmt) cc_final: 0.7222 (mmt) REVERT: A 396 MET cc_start: 0.7612 (mmm) cc_final: 0.7202 (mmp) REVERT: A 724 SER cc_start: 0.5499 (OUTLIER) cc_final: 0.5141 (p) REVERT: B 49 ASP cc_start: 0.6705 (p0) cc_final: 0.6332 (p0) REVERT: B 494 LEU cc_start: 0.8034 (tm) cc_final: 0.7736 (tp) REVERT: B 658 TRP cc_start: 0.3930 (p90) cc_final: 0.3366 (p90) REVERT: C 540 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: D 431 MET cc_start: 0.7201 (mmm) cc_final: 0.6819 (mmt) REVERT: D 540 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7264 (tt0) outliers start: 61 outliers final: 33 residues processed: 287 average time/residue: 2.0652 time to fit residues: 725.2914 Evaluate side-chains 270 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN B 735 ASN D 56 GLN D 69 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24636 Z= 0.174 Angle : 0.481 6.505 33336 Z= 0.260 Chirality : 0.040 0.145 3846 Planarity : 0.003 0.047 4288 Dihedral : 4.533 48.214 3270 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.90 % Rotamer: Outliers : 1.86 % Allowed : 16.03 % Favored : 82.11 % 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: -0.95 (0.15), residues: 3042 helix: 1.75 (0.16), residues: 1008 sheet: -0.87 (0.18), residues: 796 loop : -2.58 (0.15), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 658 HIS 0.005 0.001 HIS C 355 PHE 0.022 0.001 PHE C 26 TYR 0.012 0.001 TYR A 510 ARG 0.005 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7971 (mmt) cc_final: 0.7660 (mmt) REVERT: A 396 MET cc_start: 0.7581 (mmm) cc_final: 0.7141 (mmp) REVERT: A 571 LYS cc_start: 0.5312 (OUTLIER) cc_final: 0.4865 (mttp) REVERT: A 724 SER cc_start: 0.5518 (OUTLIER) cc_final: 0.5180 (p) REVERT: B 49 ASP cc_start: 0.6735 (p0) cc_final: 0.6440 (p0) REVERT: B 494 LEU cc_start: 0.7959 (tm) cc_final: 0.7677 (tp) REVERT: C 396 MET cc_start: 0.7210 (mmm) cc_final: 0.6776 (mmp) REVERT: C 540 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: D 540 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7241 (tt0) outliers start: 51 outliers final: 32 residues processed: 277 average time/residue: 2.0527 time to fit residues: 702.5213 Evaluate side-chains 274 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN D 56 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24636 Z= 0.305 Angle : 0.542 5.931 33336 Z= 0.296 Chirality : 0.042 0.148 3846 Planarity : 0.004 0.046 4288 Dihedral : 4.825 50.860 3270 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 2.51 % Allowed : 15.74 % Favored : 81.74 % 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: -1.14 (0.15), residues: 3042 helix: 1.41 (0.15), residues: 1012 sheet: -0.85 (0.19), residues: 808 loop : -2.63 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 658 HIS 0.009 0.001 HIS C 355 PHE 0.027 0.002 PHE C 26 TYR 0.017 0.002 TYR A 510 ARG 0.006 0.001 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6796 (mttp) REVERT: A 238 MET cc_start: 0.8002 (mmt) cc_final: 0.7653 (mmt) REVERT: A 396 MET cc_start: 0.7551 (mmm) cc_final: 0.7137 (mmp) REVERT: A 571 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5006 (mttp) REVERT: B 49 ASP cc_start: 0.6818 (p0) cc_final: 0.6405 (p0) REVERT: B 78 GLN cc_start: 0.7305 (tt0) cc_final: 0.7079 (tt0) REVERT: B 464 TYR cc_start: 0.7275 (p90) cc_final: 0.6968 (p90) REVERT: B 494 LEU cc_start: 0.8066 (tm) cc_final: 0.7782 (tp) REVERT: B 658 TRP cc_start: 0.3795 (p90) cc_final: 0.3509 (p90) REVERT: B 734 ARG cc_start: 0.6750 (ptm160) cc_final: 0.6472 (ttt90) REVERT: C 130 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6746 (mttp) REVERT: C 396 MET cc_start: 0.7236 (mmm) cc_final: 0.6897 (mmp) REVERT: C 540 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: D 540 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: D 598 GLN cc_start: 0.7880 (tt0) cc_final: 0.7661 (tm-30) REVERT: D 658 TRP cc_start: 0.5912 (OUTLIER) cc_final: 0.4284 (p90) REVERT: D 734 ARG cc_start: 0.6814 (ptm160) cc_final: 0.6480 (ttt90) outliers start: 69 outliers final: 39 residues processed: 294 average time/residue: 2.0724 time to fit residues: 745.1822 Evaluate side-chains 280 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 235 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24636 Z= 0.159 Angle : 0.476 7.412 33336 Z= 0.257 Chirality : 0.040 0.158 3846 Planarity : 0.003 0.047 4288 Dihedral : 4.538 52.247 3270 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 1.82 % Allowed : 16.95 % Favored : 81.23 % 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: -0.80 (0.15), residues: 3042 helix: 1.92 (0.16), residues: 1008 sheet: -0.78 (0.18), residues: 808 loop : -2.55 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 658 HIS 0.004 0.001 HIS C 235 PHE 0.022 0.001 PHE C 26 TYR 0.016 0.001 TYR B 464 ARG 0.007 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8128 (mmt) cc_final: 0.7814 (mmt) REVERT: A 396 MET cc_start: 0.7517 (mmm) cc_final: 0.7090 (mmp) REVERT: A 571 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.5039 (mttp) REVERT: A 724 SER cc_start: 0.5359 (OUTLIER) cc_final: 0.5045 (p) REVERT: B 49 ASP cc_start: 0.6695 (p0) cc_final: 0.6276 (p0) REVERT: B 78 GLN cc_start: 0.7436 (tt0) cc_final: 0.7231 (tt0) REVERT: B 259 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.5868 (mm-30) REVERT: B 494 LEU cc_start: 0.7957 (tm) cc_final: 0.7690 (tp) REVERT: B 734 ARG cc_start: 0.6880 (ptm160) cc_final: 0.6615 (ttt90) REVERT: C 396 MET cc_start: 0.7139 (mmm) cc_final: 0.6739 (mmp) REVERT: C 540 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: D 49 ASP cc_start: 0.6749 (p0) cc_final: 0.6292 (p0) REVERT: D 259 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.5954 (mm-30) REVERT: D 540 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7191 (tt0) outliers start: 50 outliers final: 31 residues processed: 287 average time/residue: 2.0146 time to fit residues: 711.3773 Evaluate side-chains 279 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Chi-restraints excluded: chain D residue 771 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 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 548 ASN D 56 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24636 Z= 0.258 Angle : 0.521 6.864 33336 Z= 0.283 Chirality : 0.042 0.147 3846 Planarity : 0.003 0.049 4288 Dihedral : 4.707 52.313 3270 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 1.90 % Allowed : 17.20 % Favored : 80.90 % 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: -0.97 (0.15), residues: 3042 helix: 1.65 (0.16), residues: 1012 sheet: -0.79 (0.19), residues: 808 loop : -2.58 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 658 HIS 0.007 0.001 HIS C 355 PHE 0.025 0.002 PHE C 26 TYR 0.016 0.001 TYR A 510 ARG 0.007 0.001 ARG C 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 251 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8105 (mmt) cc_final: 0.7750 (mmt) REVERT: A 396 MET cc_start: 0.7559 (mmm) cc_final: 0.7139 (mmp) REVERT: A 571 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.5134 (mttp) REVERT: B 49 ASP cc_start: 0.6778 (p0) cc_final: 0.6340 (p0) REVERT: B 78 GLN cc_start: 0.7490 (tt0) cc_final: 0.7228 (tt0) REVERT: B 259 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5886 (mm-30) REVERT: B 494 LEU cc_start: 0.8054 (tm) cc_final: 0.7780 (tp) REVERT: B 734 ARG cc_start: 0.6899 (ptm160) cc_final: 0.6698 (ttt90) REVERT: C 34 MET cc_start: 0.7075 (mtt) cc_final: 0.6815 (mtt) REVERT: C 396 MET cc_start: 0.7250 (mmm) cc_final: 0.6851 (mmp) REVERT: C 540 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: D 49 ASP cc_start: 0.6810 (p0) cc_final: 0.6327 (p0) REVERT: D 98 GLN cc_start: 0.7071 (mt0) cc_final: 0.6805 (tt0) REVERT: D 259 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5907 (mm-30) REVERT: D 540 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: D 658 TRP cc_start: 0.5811 (OUTLIER) cc_final: 0.4185 (p90) REVERT: D 734 ARG cc_start: 0.6802 (ptm160) cc_final: 0.6550 (ttt90) outliers start: 52 outliers final: 37 residues processed: 285 average time/residue: 2.1251 time to fit residues: 746.3795 Evaluate side-chains 282 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 771 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Chi-restraints excluded: chain D residue 771 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN D 56 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24636 Z= 0.328 Angle : 0.564 6.068 33336 Z= 0.308 Chirality : 0.043 0.148 3846 Planarity : 0.004 0.050 4288 Dihedral : 5.013 55.008 3270 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.76 % Favored : 92.18 % Rotamer: Outliers : 1.86 % Allowed : 17.42 % Favored : 80.72 % 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: -1.23 (0.15), residues: 3042 helix: 1.27 (0.15), residues: 1014 sheet: -0.82 (0.19), residues: 804 loop : -2.67 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 658 HIS 0.010 0.001 HIS C 355 PHE 0.028 0.002 PHE C 26 TYR 0.018 0.002 TYR A 510 ARG 0.006 0.001 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 255 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8111 (mmt) cc_final: 0.7726 (mmt) REVERT: A 396 MET cc_start: 0.7571 (mmm) cc_final: 0.7161 (mmp) REVERT: A 571 LYS cc_start: 0.5583 (OUTLIER) cc_final: 0.5283 (mttp) REVERT: A 720 ARG cc_start: 0.6766 (tpt-90) cc_final: 0.6561 (mmt90) REVERT: B 49 ASP cc_start: 0.6989 (p0) cc_final: 0.6468 (p0) REVERT: B 494 LEU cc_start: 0.8112 (tm) cc_final: 0.7832 (tp) REVERT: C 396 MET cc_start: 0.7237 (mmm) cc_final: 0.6853 (mmp) REVERT: D 98 GLN cc_start: 0.7125 (mt0) cc_final: 0.6823 (tt0) REVERT: D 456 LYS cc_start: 0.7677 (mppt) cc_final: 0.7372 (mptp) REVERT: D 540 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: D 658 TRP cc_start: 0.5867 (OUTLIER) cc_final: 0.4148 (p90) REVERT: D 734 ARG cc_start: 0.6807 (ptm160) cc_final: 0.6566 (ttt90) outliers start: 51 outliers final: 33 residues processed: 289 average time/residue: 2.1710 time to fit residues: 766.8175 Evaluate side-chains 273 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 771 GLN Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 658 TRP Chi-restraints excluded: chain D residue 771 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.2980 chunk 256 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 241 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.228295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.172748 restraints weight = 79972.731| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.01 r_work: 0.3877 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24636 Z= 0.164 Angle : 0.483 6.231 33336 Z= 0.261 Chirality : 0.040 0.146 3846 Planarity : 0.003 0.075 4288 Dihedral : 4.650 55.793 3270 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 93.00 % Rotamer: Outliers : 1.28 % Allowed : 18.40 % Favored : 80.32 % 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: -0.81 (0.15), residues: 3042 helix: 1.85 (0.16), residues: 1008 sheet: -0.73 (0.19), residues: 778 loop : -2.51 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 658 HIS 0.005 0.001 HIS A 235 PHE 0.022 0.001 PHE C 16 TYR 0.016 0.001 TYR B 464 ARG 0.008 0.000 ARG C 720 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14776.07 seconds wall clock time: 259 minutes 46.56 seconds (15586.56 seconds total)