Starting phenix.real_space_refine (version: dev) on Thu May 12 19:51:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu2_32817/05_2022/7wu2_32817.pdb" } resolution = 2.8 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= 0.002 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 "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2115 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 269} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 5.08, per 1000 atoms: 0.65 Number of scatterers: 7829 At special positions: 0 Unit cell: (106.029, 118.881, 83.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1450 8.00 N 1361 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 40.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.904A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.675A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.196A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.860A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.613A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.733A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.305A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.503A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 559 through 591 Processing helix chain 'R' and resid 592 through 594 No H-bonds generated for 'chain 'R' and resid 592 through 594' Processing helix chain 'R' and resid 601 through 623 Processing helix chain 'R' and resid 629 through 662 removed outlier: 4.006A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 646 " --> pdb=" O PHE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 680 Processing helix chain 'R' and resid 680 through 694 removed outlier: 3.706A pdb=" N LEU R 684 " --> pdb=" O TRP R 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 737 Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 738 through 745 Processing helix chain 'R' and resid 745 through 750 removed outlier: 4.002A pdb=" N HIS R 749 " --> pdb=" O ASN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 752 through 764 removed outlier: 3.967A pdb=" N LYS R 756 " --> pdb=" O PRO R 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 757 " --> pdb=" O SER R 753 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 758 " --> pdb=" O ALA R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 770 removed outlier: 4.572A pdb=" N ILE R 768 " --> pdb=" O VAL R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 778 removed outlier: 3.822A pdb=" N VAL R 777 " --> pdb=" O TRP R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 779 through 781 No H-bonds generated for 'chain 'R' and resid 779 through 781' Processing helix chain 'R' and resid 783 through 797 removed outlier: 3.647A pdb=" N PHE R 787 " --> pdb=" O CYS R 783 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 807 Processing helix chain 'R' and resid 810 through 821 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.251A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.759A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.714A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.393A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.046A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2552 1.34 - 1.46: 1364 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 7992 Sorted by residual: bond pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.23e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" N TYR A 253 " pdb=" CA TYR A 253 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.84e+00 bond pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.02e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.71: 110 105.71 - 112.80: 4282 112.80 - 119.90: 2627 119.90 - 126.99: 3735 126.99 - 134.09: 91 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASP A 49 " pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CB ARG B 8 " pdb=" CG ARG B 8 " pdb=" CD ARG B 8 " ideal model delta sigma weight residual 111.30 119.21 -7.91 2.30e+00 1.89e-01 1.18e+01 angle pdb=" C ASN R 546 " pdb=" N PHE R 547 " pdb=" CA PHE R 547 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.28 114.62 -4.34 1.55e+00 4.16e-01 7.84e+00 angle pdb=" N ASN A 50 " pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 110.49 115.04 -4.55 1.69e+00 3.50e-01 7.25e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4345 17.88 - 35.75: 321 35.75 - 53.63: 47 53.63 - 71.51: 9 71.51 - 89.38: 7 Dihedral angle restraints: 4729 sinusoidal: 1800 harmonic: 2929 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual -86.00 -132.06 46.06 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.57 -43.43 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 876 0.037 - 0.075: 263 0.075 - 0.112: 73 0.112 - 0.149: 22 0.149 - 0.186: 2 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA THR R 630 " pdb=" N THR R 630 " pdb=" C THR R 630 " pdb=" CB THR R 630 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1233 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ASP A 49 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 50 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASP A 252 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 252 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 253 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 598 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG R 598 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG R 598 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN R 599 " 0.008 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 7936 3.28 - 3.82: 13282 3.82 - 4.36: 15829 4.36 - 4.90: 27202 Nonbonded interactions: 64765 Sorted by model distance: nonbonded pdb=" O THR R 596 " pdb=" ND2 ASN R 599 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.217 2.440 nonbonded pdb=" O ASP R 696 " pdb=" OG1 THR R 700 " model vdw 2.262 2.440 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.307 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.314 2.440 ... (remaining 64760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4968 2.51 5 N 1361 2.21 5 O 1450 1.98 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.930 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 0.031 7992 Z= 0.130 Angle : 0.513 9.441 10845 Z= 0.275 Chirality : 0.041 0.186 1236 Planarity : 0.003 0.040 1385 Dihedral : 12.858 89.384 2828 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.00 % 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: 0.79 (0.27), residues: 998 helix: 1.38 (0.29), residues: 369 sheet: 0.65 (0.34), residues: 224 loop : -0.27 (0.31), residues: 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.9674 time to fit residues: 161.0172 Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 32 GLN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 562 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7992 Z= 0.239 Angle : 0.554 7.742 10845 Z= 0.292 Chirality : 0.043 0.147 1236 Planarity : 0.004 0.041 1385 Dihedral : 4.187 27.023 1095 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 998 helix: 2.04 (0.29), residues: 356 sheet: 0.53 (0.34), residues: 221 loop : -0.12 (0.31), residues: 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.953 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 131 average time/residue: 0.8876 time to fit residues: 125.6721 Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.4680 time to fit residues: 3.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 7992 Z= 0.317 Angle : 0.601 10.766 10845 Z= 0.320 Chirality : 0.044 0.164 1236 Planarity : 0.004 0.058 1385 Dihedral : 4.574 33.302 1095 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 998 helix: 1.73 (0.28), residues: 363 sheet: 0.34 (0.33), residues: 221 loop : -0.36 (0.31), residues: 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 0.943 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 139 average time/residue: 0.9045 time to fit residues: 135.6522 Evaluate side-chains 124 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.4366 time to fit residues: 4.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS R 788 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7992 Z= 0.279 Angle : 0.568 10.682 10845 Z= 0.304 Chirality : 0.043 0.151 1236 Planarity : 0.005 0.100 1385 Dihedral : 4.501 31.949 1095 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.69 (0.27), residues: 998 helix: 1.77 (0.28), residues: 360 sheet: 0.33 (0.34), residues: 215 loop : -0.58 (0.30), residues: 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 106 time to evaluate : 0.936 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 131 average time/residue: 0.9170 time to fit residues: 129.6252 Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.6758 time to fit residues: 5.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS R 600 GLN R 788 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7992 Z= 0.297 Angle : 0.579 11.841 10845 Z= 0.310 Chirality : 0.043 0.154 1236 Planarity : 0.004 0.067 1385 Dihedral : 4.586 31.769 1095 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer Outliers : 5.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 998 helix: 1.64 (0.27), residues: 363 sheet: 0.38 (0.34), residues: 212 loop : -0.66 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 0.947 Fit side-chains outliers start: 42 outliers final: 26 residues processed: 132 average time/residue: 0.9452 time to fit residues: 134.4492 Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.4535 time to fit residues: 4.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7992 Z= 0.272 Angle : 0.563 11.213 10845 Z= 0.301 Chirality : 0.043 0.149 1236 Planarity : 0.004 0.056 1385 Dihedral : 4.527 32.132 1095 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.62 (0.26), residues: 998 helix: 1.73 (0.27), residues: 362 sheet: 0.34 (0.35), residues: 212 loop : -0.67 (0.30), residues: 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 0.939 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 127 average time/residue: 0.8882 time to fit residues: 122.0063 Evaluate side-chains 121 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.4305 time to fit residues: 3.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 chunk 94 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 7992 Z= 0.159 Angle : 0.488 8.775 10845 Z= 0.262 Chirality : 0.040 0.141 1236 Planarity : 0.003 0.057 1385 Dihedral : 4.188 32.036 1095 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.86 (0.27), residues: 998 helix: 2.05 (0.28), residues: 362 sheet: 0.29 (0.35), residues: 214 loop : -0.57 (0.30), residues: 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.899 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 24 residues processed: 132 average time/residue: 0.9512 time to fit residues: 135.3164 Evaluate side-chains 123 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.1456 time to fit residues: 1.8930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 7992 Z= 0.368 Angle : 0.640 12.097 10845 Z= 0.336 Chirality : 0.045 0.169 1236 Planarity : 0.005 0.095 1385 Dihedral : 4.657 32.120 1095 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 998 helix: 1.64 (0.27), residues: 362 sheet: 0.20 (0.33), residues: 221 loop : -0.66 (0.30), residues: 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 0.890 Fit side-chains outliers start: 34 outliers final: 24 residues processed: 120 average time/residue: 0.9677 time to fit residues: 125.1198 Evaluate side-chains 120 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.1253 time to fit residues: 1.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7992 Z= 0.228 Angle : 0.556 10.467 10845 Z= 0.293 Chirality : 0.042 0.145 1236 Planarity : 0.004 0.080 1385 Dihedral : 4.428 32.401 1095 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.66 (0.27), residues: 998 helix: 1.81 (0.27), residues: 362 sheet: 0.23 (0.34), residues: 212 loop : -0.63 (0.30), residues: 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.918 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 121 average time/residue: 0.9728 time to fit residues: 126.9285 Evaluate side-chains 116 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.2469 time to fit residues: 1.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 562 HIS ** R 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7992 Z= 0.190 Angle : 0.526 9.361 10845 Z= 0.277 Chirality : 0.041 0.141 1236 Planarity : 0.004 0.076 1385 Dihedral : 4.254 32.121 1095 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.27), residues: 998 helix: 1.98 (0.28), residues: 362 sheet: 0.16 (0.34), residues: 215 loop : -0.57 (0.30), residues: 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.016 Fit side-chains outliers start: 23 outliers final: 22 residues processed: 118 average time/residue: 1.1156 time to fit residues: 142.0281 Evaluate side-chains 120 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.1629 time to fit residues: 2.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124322 restraints weight = 8097.437| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.99 r_work: 0.3418 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work: 0.3376 rms_B_bonded: 1.87 restraints_weight: 0.1250 r_work: 0.3351 rms_B_bonded: 2.07 restraints_weight: 0.0625 r_work: 0.3321 rms_B_bonded: 2.36 restraints_weight: 0.0312 r_work: 0.3286 rms_B_bonded: 2.77 restraints_weight: 0.0156 r_work: 0.3243 rms_B_bonded: 3.33 restraints_weight: 0.0078 r_work: 0.3188 rms_B_bonded: 4.11 restraints_weight: 0.0039 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7992 Z= 0.202 Angle : 0.531 9.534 10845 Z= 0.279 Chirality : 0.041 0.156 1236 Planarity : 0.004 0.074 1385 Dihedral : 4.251 32.104 1095 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.78 (0.27), residues: 998 helix: 2.00 (0.27), residues: 362 sheet: 0.14 (0.34), residues: 215 loop : -0.55 (0.30), residues: 421 =============================================================================== Job complete usr+sys time: 2679.65 seconds wall clock time: 48 minutes 34.77 seconds (2914.77 seconds total)