Starting phenix.real_space_refine (version: dev) on Thu Dec 22 09:26:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/12_2022/6tfj_10492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/12_2022/6tfj_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_10492/12_2022/6tfj_10492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/12_2022/6tfj_10492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/12_2022/6tfj_10492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfj_10492/12_2022/6tfj_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 Convert atoms to be neutral 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-4807/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: 21.36, per 1000 atoms: 0.44 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: 37.58 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: 1.49 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: 19.07 Time building geometry restraints manager: 39.04 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 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. 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: 0.620 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: 8.380 Check model and map are aligned: 0.760 Convert atoms to be neutral: 0.430 Process input model: 139.110 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 3.739 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: 2.0851 time to fit residues: 1205.0057 Evaluate side-chains 281 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 276 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 4 average time/residue: 0.7083 time to fit residues: 9.1689 ------------------------------------------------------------------------------- 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: 0.7448 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 : 3.898 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: 1.9953 time to fit residues: 798.1094 Evaluate side-chains 283 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 264 time to evaluate : 4.291 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 8 residues processed: 11 average time/residue: 0.5951 time to fit residues: 17.7139 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 0.5980 chunk 221 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.2564 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= 0.208 Angle : 0.493 4.743 33336 Z= 0.266 Chirality : 0.041 0.144 3846 Planarity : 0.003 0.044 4288 Dihedral : 4.341 20.424 3266 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.90 % Rotamer Outliers : 2.04 % 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: -1.43 (0.15), residues: 3042 helix: 1.32 (0.16), residues: 1020 sheet: -1.18 (0.18), residues: 816 loop : -2.83 (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 324 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 3.883 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 outliers start: 56 outliers final: 27 residues processed: 297 average time/residue: 1.9582 time to fit residues: 727.3014 Evaluate side-chains 275 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 248 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 15 residues processed: 12 average time/residue: 0.5634 time to fit residues: 16.9825 ------------------------------------------------------------------------------- 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: 0.3980 chunk 131 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24636 Z= 0.188 Angle : 0.476 5.010 33336 Z= 0.257 Chirality : 0.040 0.142 3846 Planarity : 0.003 0.044 4288 Dihedral : 4.289 20.798 3266 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer Outliers : 2.04 % 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: 1.60 (0.16), residues: 1020 sheet: -1.04 (0.18), residues: 810 loop : -2.68 (0.15), residues: 1212 *********************** 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 324 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 3.931 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: 56 outliers final: 30 residues processed: 300 average time/residue: 1.9037 time to fit residues: 707.7660 Evaluate side-chains 278 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 19 residues processed: 11 average time/residue: 0.5086 time to fit residues: 15.3310 ------------------------------------------------------------------------------- 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: 3.9990 chunk 4 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 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: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 C 771 GLN D 56 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 24636 Z= 0.335 Angle : 0.570 6.719 33336 Z= 0.311 Chirality : 0.043 0.148 3846 Planarity : 0.003 0.043 4288 Dihedral : 4.773 29.234 3266 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.66 % Favored : 92.27 % Rotamer Outliers : 2.59 % 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: -1.38 (0.15), residues: 3042 helix: 1.12 (0.15), residues: 1024 sheet: -0.96 (0.18), residues: 832 loop : -2.76 (0.15), residues: 1186 *********************** 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 339 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 268 time to evaluate : 3.967 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: 71 outliers final: 32 residues processed: 310 average time/residue: 1.9129 time to fit residues: 741.2952 Evaluate side-chains 279 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 16 residues processed: 16 average time/residue: 0.6831 time to fit residues: 23.0881 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** B 163 ASN D 56 GLN ** 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: 0.7486 moved from start: 0.3437 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= 0.199 Angle : 0.497 6.483 33336 Z= 0.269 Chirality : 0.041 0.145 3846 Planarity : 0.003 0.045 4288 Dihedral : 4.527 26.546 3266 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer Outliers : 1.97 % 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: -1.09 (0.15), residues: 3042 helix: 1.53 (0.16), residues: 1020 sheet: -0.89 (0.18), residues: 800 loop : -2.63 (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 314 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 3.818 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: 54 outliers final: 33 residues processed: 295 average time/residue: 1.8655 time to fit residues: 685.2542 Evaluate side-chains 278 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 22 residues processed: 11 average time/residue: 0.5670 time to fit residues: 15.4407 ------------------------------------------------------------------------------- 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: 4.9990 chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** D 56 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3691 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= 0.292 Angle : 0.537 6.086 33336 Z= 0.292 Chirality : 0.042 0.146 3846 Planarity : 0.003 0.044 4288 Dihedral : 4.709 28.301 3266 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer Outliers : 2.22 % 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: -1.19 (0.15), residues: 3042 helix: 1.35 (0.16), residues: 1024 sheet: -0.88 (0.18), residues: 810 loop : -2.69 (0.15), residues: 1208 *********************** 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 310 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 3.588 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: 61 outliers final: 40 residues processed: 287 average time/residue: 1.8885 time to fit residues: 683.5073 Evaluate side-chains 280 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 14 average time/residue: 0.7620 time to fit residues: 22.1349 ------------------------------------------------------------------------------- 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: 0.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** 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: 0.7498 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24636 Z= 0.220 Angle : 0.505 6.322 33336 Z= 0.273 Chirality : 0.041 0.160 3846 Planarity : 0.003 0.046 4288 Dihedral : 4.589 26.720 3266 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % 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: -1.04 (0.15), residues: 3042 helix: 1.55 (0.16), residues: 1024 sheet: -0.84 (0.18), residues: 810 loop : -2.64 (0.16), residues: 1208 *********************** 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: 49 poor density : 255 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 outliers start: 49 outliers final: 38 residues processed: 289 average time/residue: 1.8456 time to fit residues: 667.4473 Evaluate side-chains 281 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 27 residues processed: 11 average time/residue: 0.6788 time to fit residues: 17.8160 ------------------------------------------------------------------------------- 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: 6.9990 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 273 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 B 69 ASN D 56 GLN ** 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: 0.7491 moved from start: 0.3837 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= 0.198 Angle : 0.497 8.380 33336 Z= 0.268 Chirality : 0.041 0.146 3846 Planarity : 0.003 0.068 4288 Dihedral : 4.518 24.918 3266 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.40 % Favored : 92.54 % 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: -0.93 (0.15), residues: 3042 helix: 1.74 (0.16), residues: 1012 sheet: -0.80 (0.18), residues: 814 loop : -2.60 (0.16), residues: 1216 *********************** 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 290 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 3.775 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: 44 outliers final: 36 residues processed: 278 average time/residue: 1.8625 time to fit residues: 650.4704 Evaluate side-chains 275 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 3.699 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.6436 time to fit residues: 13.6601 ------------------------------------------------------------------------------- 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: 20.0000 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 0.0040 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 78 GLN D 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 24636 Z= 0.242 Angle : 0.515 8.137 33336 Z= 0.279 Chirality : 0.041 0.146 3846 Planarity : 0.003 0.050 4288 Dihedral : 4.600 25.526 3266 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer Outliers : 1.53 % 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: -0.99 (0.15), residues: 3042 helix: 1.62 (0.16), residues: 1012 sheet: -0.78 (0.18), residues: 810 loop : -2.62 (0.15), residues: 1220 ********************** 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 285 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 3.998 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 outliers start: 42 outliers final: 33 residues processed: 274 average time/residue: 1.9332 time to fit residues: 667.8429 Evaluate side-chains 269 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 3.684 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.7843 time to fit residues: 11.3727 ------------------------------------------------------------------------------- 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: 0.9990 chunk 256 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 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: 0.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN D 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.229066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.174985 restraints weight = 79955.533| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.86 r_work: 0.3877 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24636 Z= 0.162 Angle : 0.475 6.902 33336 Z= 0.256 Chirality : 0.040 0.145 3846 Planarity : 0.003 0.051 4288 Dihedral : 4.397 22.705 3266 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer Outliers : 1.38 % 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: -0.74 (0.15), residues: 3042 helix: 1.94 (0.16), residues: 1012 sheet: -0.75 (0.18), residues: 800 loop : -2.49 (0.16), residues: 1230 =============================================================================== Job complete usr+sys time: 13753.49 seconds wall clock time: 241 minutes 26.15 seconds (14486.15 seconds total)