Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 00:11:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/07_2023/6tfj_10492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/07_2023/6tfj_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_10492/07_2023/6tfj_10492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/07_2023/6tfj_10492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/07_2023/6tfj_10492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/07_2023/6tfj_10492.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-5013/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: 18.33, per 1000 atoms: 0.38 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: 38.47 Conformation dependent library (CDL) restraints added in 3.8 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: 1.60 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: 20.31 Time building geometry restraints manager: 39.74 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: 18605 16.88 - 33.76: 752 33.76 - 50.64: 118 50.64 - 67.52: 48 67.52 - 84.40: 9 Dihedral angle restraints: 19532 sinusoidal: 9222 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 19529 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: 0.820 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: 0.730 Extract box with map and model: 7.970 Check model and map are aligned: 0.670 Set scattering table: 0.360 Process input model: 139.480 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.830 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.674 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 outliers start: 3 outliers final: 5 residues processed: 477 average time/residue: 2.3773 time to fit residues: 1350.3219 Evaluate side-chains 281 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 276 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 4 average time/residue: 0.7473 time to fit residues: 9.4976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 24636 Z= 0.277 Angle : 0.535 5.345 33336 Z= 0.289 Chirality : 0.042 0.151 3846 Planarity : 0.003 0.047 4288 Dihedral : 4.381 21.878 3266 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.70 % Rotamer Outliers : 1.79 % 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: -1.82 (0.14), residues: 3042 helix: 0.88 (0.15), residues: 1020 sheet: -1.37 (0.17), residues: 790 loop : -2.94 (0.15), residues: 1232 *********************** 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 344 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 295 time to evaluate : 3.692 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 outliers start: 49 outliers final: 19 residues processed: 324 average time/residue: 2.1478 time to fit residues: 844.9809 Evaluate side-chains 283 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 264 time to evaluate : 3.726 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 8 residues processed: 11 average time/residue: 0.5512 time to fit residues: 16.0413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.7264 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24636 Z= 0.216 Angle : 0.498 4.825 33336 Z= 0.269 Chirality : 0.041 0.144 3846 Planarity : 0.003 0.041 4288 Dihedral : 4.363 21.082 3266 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.06 % Rotamer Outliers : 2.11 % 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: -1.42 (0.15), residues: 3042 helix: 1.31 (0.16), residues: 1020 sheet: -1.17 (0.18), residues: 816 loop : -2.82 (0.15), residues: 1206 *********************** 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 330 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 3.951 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 outliers start: 58 outliers final: 27 residues processed: 302 average time/residue: 2.1221 time to fit residues: 785.7678 Evaluate side-chains 278 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 11 average time/residue: 0.5694 time to fit residues: 16.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 79 optimal weight: 0.0060 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 163 ASN D 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 24636 Z= 0.150 Angle : 0.461 6.308 33336 Z= 0.248 Chirality : 0.040 0.142 3846 Planarity : 0.003 0.044 4288 Dihedral : 4.182 19.507 3266 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.66 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3042 helix: 1.77 (0.16), residues: 1020 sheet: -0.99 (0.18), residues: 798 loop : -2.63 (0.15), residues: 1224 *********************** 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 325 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 3.859 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: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 300 average time/residue: 2.1056 time to fit residues: 773.8428 Evaluate side-chains 281 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 18 residues processed: 12 average time/residue: 0.7804 time to fit residues: 19.7487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 121 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 GLN D 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 24636 Z= 0.354 Angle : 0.571 7.989 33336 Z= 0.312 Chirality : 0.043 0.149 3846 Planarity : 0.004 0.044 4288 Dihedral : 4.739 28.322 3266 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer Outliers : 2.55 % 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: -1.37 (0.15), residues: 3042 helix: 1.14 (0.15), residues: 1026 sheet: -1.00 (0.18), residues: 852 loop : -2.76 (0.16), residues: 1164 *********************** 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 335 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 265 time to evaluate : 3.865 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 outliers start: 70 outliers final: 32 residues processed: 310 average time/residue: 2.1018 time to fit residues: 805.7440 Evaluate side-chains 273 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 3.668 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 17 residues processed: 15 average time/residue: 0.6187 time to fit residues: 21.2732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24636 Z= 0.179 Angle : 0.486 5.974 33336 Z= 0.262 Chirality : 0.040 0.145 3846 Planarity : 0.003 0.050 4288 Dihedral : 4.449 25.186 3266 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.03 % Rotamer Outliers : 1.79 % 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: -1.01 (0.15), residues: 3042 helix: 1.65 (0.16), residues: 1020 sheet: -0.89 (0.18), residues: 800 loop : -2.61 (0.15), residues: 1222 *********************** 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 304 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 255 time to evaluate : 3.777 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 outliers start: 49 outliers final: 29 residues processed: 287 average time/residue: 2.2131 time to fit residues: 796.9215 Evaluate side-chains 270 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 3.675 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.7069 time to fit residues: 14.2426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 247 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** D 56 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 24636 Z= 0.233 Angle : 0.504 6.222 33336 Z= 0.273 Chirality : 0.041 0.145 3846 Planarity : 0.003 0.050 4288 Dihedral : 4.512 25.120 3266 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.41 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3042 helix: 1.59 (0.16), residues: 1024 sheet: -0.85 (0.18), residues: 812 loop : -2.63 (0.16), residues: 1206 *********************** 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 295 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 4.239 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 outliers start: 51 outliers final: 33 residues processed: 276 average time/residue: 2.0584 time to fit residues: 695.7580 Evaluate side-chains 266 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 3.813 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 21 residues processed: 12 average time/residue: 0.6165 time to fit residues: 17.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.0570 chunk 186 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN D 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3564 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= 0.152 Angle : 0.468 6.374 33336 Z= 0.251 Chirality : 0.040 0.159 3846 Planarity : 0.003 0.048 4288 Dihedral : 4.301 21.117 3266 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Rotamer Outliers : 1.60 % 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: -0.77 (0.15), residues: 3042 helix: 1.94 (0.16), residues: 1020 sheet: -0.80 (0.18), residues: 812 loop : -2.54 (0.16), residues: 1210 *********************** 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 289 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 3.443 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 outliers start: 44 outliers final: 28 residues processed: 278 average time/residue: 2.0436 time to fit residues: 710.0271 Evaluate side-chains 263 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.7255 time to fit residues: 12.3055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 5.9990 chunk 280 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 24636 Z= 0.173 Angle : 0.477 6.361 33336 Z= 0.256 Chirality : 0.040 0.147 3846 Planarity : 0.003 0.049 4288 Dihedral : 4.283 20.399 3266 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 93.00 % Rotamer Outliers : 1.49 % 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: -0.70 (0.15), residues: 3042 helix: 2.02 (0.16), residues: 1010 sheet: -0.72 (0.18), residues: 798 loop : -2.50 (0.16), residues: 1234 *********************** 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 284 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 3.700 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 outliers start: 41 outliers final: 34 residues processed: 274 average time/residue: 2.0572 time to fit residues: 694.1204 Evaluate side-chains 269 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 8 average time/residue: 0.6637 time to fit residues: 14.0516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN B 78 GLN C 407 GLN D 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24636 Z= 0.192 Angle : 0.484 8.485 33336 Z= 0.260 Chirality : 0.040 0.146 3846 Planarity : 0.003 0.060 4288 Dihedral : 4.328 21.150 3266 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.97 % Rotamer Outliers : 1.35 % 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: -0.71 (0.15), residues: 3042 helix: 1.97 (0.16), residues: 1010 sheet: -0.67 (0.19), residues: 778 loop : -2.49 (0.16), residues: 1254 ********************** 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 277 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 240 time to evaluate : 3.710 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 outliers start: 37 outliers final: 29 residues processed: 273 average time/residue: 2.0998 time to fit residues: 711.0203 Evaluate side-chains 263 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 3.456 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.7566 time to fit residues: 9.4981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 73 optimal weight: 0.0040 chunk 222 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 D 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.230339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.176646 restraints weight = 79954.240| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.93 r_work: 0.3895 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24636 Z= 0.149 Angle : 0.465 7.838 33336 Z= 0.249 Chirality : 0.040 0.144 3846 Planarity : 0.003 0.053 4288 Dihedral : 4.200 20.485 3266 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.23 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3042 helix: 2.17 (0.16), residues: 1008 sheet: -0.63 (0.19), residues: 778 loop : -2.43 (0.16), residues: 1256 =============================================================================== Job complete usr+sys time: 14393.70 seconds wall clock time: 255 minutes 21.47 seconds (15321.47 seconds total)