Starting phenix.real_space_refine (version: dev) on Mon Dec 12 03:26:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2022/6pw9_20501_updated.pdb" } resolution = 4.03 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 ARG 62": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 825": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8836 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1260 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5470 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1287 Unusual residues: {'ACE': 1} Classifications: {'peptide': 160, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'ACO': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.91, per 1000 atoms: 0.67 Number of scatterers: 8836 At special positions: 0 Unit cell: (114.562, 100.534, 106.379, 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 56 16.00 P 9 15.00 O 1666 8.00 N 1508 7.00 C 5597 6.00 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: 3.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 3 sheets defined 57.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 165 through 175 removed outlier: 4.139A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.824A pdb=" N ILE B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.066A pdb=" N PHE B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.627A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 4.043A pdb=" N PHE B 326 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 356 removed outlier: 4.479A pdb=" N SER B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.276A pdb=" N THR B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.866A pdb=" N TYR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.806A pdb=" N GLU B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 502 through 524 removed outlier: 5.415A pdb=" N GLN B 522 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 536 through 546 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 552 through 570 removed outlier: 4.124A pdb=" N ILE B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 647 No H-bonds generated for 'chain 'B' and resid 644 through 647' Processing helix chain 'B' and resid 654 through 667 Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 688 through 699 Processing helix chain 'B' and resid 706 through 721 Processing helix chain 'B' and resid 728 through 741 removed outlier: 3.732A pdb=" N THR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 Processing helix chain 'B' and resid 762 through 774 removed outlier: 3.797A pdb=" N MET B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 786 removed outlier: 3.529A pdb=" N GLN B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 784 " --> pdb=" O LYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 810 Processing helix chain 'B' and resid 821 through 831 removed outlier: 3.824A pdb=" N LYS B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.068A pdb=" N MET C 12 " --> pdb=" O PRO C 8 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'D' and resid 61 through 84 removed outlier: 3.961A pdb=" N VAL D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 121 through 128 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.222A pdb=" N PHE A 51 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 62 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 74 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP A 64 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 72 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER A 66 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN A 108 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 74 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR A 110 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR A 76 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N HIS A 112 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N GLY A 78 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 15.201A pdb=" N GLN A 114 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 133 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 151 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 131 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.362A pdb=" N LYS C 59 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 72 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU C 61 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY C 70 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 106 through 112 removed outlier: 3.685A pdb=" N GLU C 132 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS C 148 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE C 130 " --> pdb=" O LYS C 148 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1191 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: 2.46 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1481 1.30 - 1.43: 2253 1.43 - 1.56: 5168 1.56 - 1.69: 15 1.69 - 1.82: 91 Bond restraints: 9008 Sorted by residual: bond pdb=" C1B ACO C 902 " pdb=" O4B ACO C 902 " ideal model delta sigma weight residual 1.416 1.660 -0.244 1.40e-02 5.10e+03 3.05e+02 bond pdb=" C1B ACO C 902 " pdb=" C2B ACO C 902 " ideal model delta sigma weight residual 1.531 1.345 0.186 1.20e-02 6.94e+03 2.39e+02 bond pdb=" C5P ACO C 902 " pdb=" N4P ACO C 902 " ideal model delta sigma weight residual 1.331 1.498 -0.167 1.20e-02 6.94e+03 1.93e+02 bond pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 1.337 1.463 -0.126 1.00e-02 1.00e+04 1.58e+02 bond pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 1.592 1.723 -0.131 1.10e-02 8.26e+03 1.43e+02 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.01: 176 106.01 - 113.25: 4703 113.25 - 120.49: 4160 120.49 - 127.73: 3058 127.73 - 134.97: 63 Bond angle restraints: 12160 Sorted by residual: angle pdb=" P1A ACO C 902 " pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 136.83 121.67 15.16 1.00e+00 1.00e+00 2.30e+02 angle pdb=" N1A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 118.11 104.50 13.61 1.23e+00 6.64e-01 1.23e+02 angle pdb=" C5A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 123.59 134.97 -11.38 1.08e+00 8.64e-01 1.12e+02 angle pdb=" N1A ACO C 902 " pdb=" C2A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 128.69 119.33 9.36 1.00e+00 1.00e+00 8.76e+01 angle pdb=" C5A ACO C 902 " pdb=" C4A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 126.80 118.30 8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 4892 15.16 - 30.33: 455 30.33 - 45.49: 141 45.49 - 60.65: 16 60.65 - 75.82: 6 Dihedral angle restraints: 5510 sinusoidal: 2307 harmonic: 3203 Sorted by residual: dihedral pdb=" CA LYS B 500 " pdb=" C LYS B 500 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL B 185 " pdb=" C VAL B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 102 " pdb=" C PHE C 102 " pdb=" N ASN C 103 " pdb=" CA ASN C 103 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 1324 1.011 - 2.022: 0 2.022 - 3.034: 0 3.034 - 4.045: 0 4.045 - 5.056: 3 Chirality restraints: 1327 Sorted by residual: chirality pdb=" C4 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" C5 IHP C 901 " pdb=" O14 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.58 5.06 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C2 IHP C 901 " pdb=" C1 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" O12 IHP C 901 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C1 IHP C 901 " pdb=" C2 IHP C 901 " pdb=" C6 IHP C 901 " pdb=" O11 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1324 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 143 " -0.100 5.00e-02 4.00e+02 1.49e-01 3.56e+01 pdb=" N PRO A 144 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 707 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP B 707 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 707 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 707 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 707 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 565 " 0.015 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR B 565 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 565 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 565 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 565 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 565 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 565 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 565 " 0.001 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 15 2.40 - 3.03: 4199 3.03 - 3.65: 13982 3.65 - 4.28: 19123 4.28 - 4.90: 30446 Nonbonded interactions: 67765 Sorted by model distance: nonbonded pdb=" O PRO A 13 " pdb=" CD1 ILE A 16 " model vdw 1.781 3.460 nonbonded pdb=" OE2 GLU B 191 " pdb=" O ILE B 533 " model vdw 1.914 3.040 nonbonded pdb=" O GLU A 143 " pdb=" OE1 GLU A 143 " model vdw 1.918 3.040 nonbonded pdb=" CE2 TYR B 528 " pdb=" CE LYS B 532 " model vdw 2.180 3.740 nonbonded pdb=" O ILE B 784 " pdb=" OG1 THR B 788 " model vdw 2.260 2.440 ... (remaining 67760 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 56 5.16 5 C 5597 2.51 5 N 1508 2.21 5 O 1666 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 group one per residue 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: 0.510 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: 0.010 Extract box with map and model: 2.840 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.007 0.244 9008 Z= 0.520 Angle : 1.225 15.157 12160 Z= 0.667 Chirality : 0.244 5.056 1327 Planarity : 0.008 0.149 1549 Dihedral : 13.120 75.816 3432 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 1.81 % 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: -4.47 (0.20), residues: 1065 helix: -2.86 (0.15), residues: 637 sheet: -2.24 (0.57), residues: 71 loop : -2.92 (0.27), residues: 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 302 time to evaluate : 1.108 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 outliers start: 17 outliers final: 5 residues processed: 316 average time/residue: 0.2390 time to fit residues: 98.7268 Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1535 time to fit residues: 2.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 9.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 65 HIS A 114 GLN A 148 HIS A 151 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 197 ASN B 212 HIS ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS C 120 HIS D 116 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9008 Z= 0.175 Angle : 0.735 9.885 12160 Z= 0.361 Chirality : 0.047 0.361 1327 Planarity : 0.005 0.066 1549 Dihedral : 7.127 58.043 1204 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 1065 helix: -1.49 (0.19), residues: 642 sheet: -2.06 (0.58), residues: 62 loop : -2.30 (0.29), residues: 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 1.114 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 outliers start: 7 outliers final: 2 residues processed: 255 average time/residue: 0.2118 time to fit residues: 73.6072 Evaluate side-chains 178 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0828 time to fit residues: 1.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN B 736 GLN ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9008 Z= 0.225 Angle : 0.728 8.725 12160 Z= 0.367 Chirality : 0.047 0.261 1327 Planarity : 0.005 0.044 1549 Dihedral : 6.818 59.996 1204 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1065 helix: -0.99 (0.19), residues: 648 sheet: -1.72 (0.63), residues: 65 loop : -2.13 (0.30), residues: 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.155 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 outliers start: 2 outliers final: 1 residues processed: 237 average time/residue: 0.2157 time to fit residues: 70.0860 Evaluate side-chains 185 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0843 time to fit residues: 1.7156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.0060 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 509 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS D 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9008 Z= 0.185 Angle : 0.703 8.184 12160 Z= 0.351 Chirality : 0.046 0.229 1327 Planarity : 0.004 0.043 1549 Dihedral : 6.634 59.235 1204 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -1.88 (0.24), residues: 1065 helix: -0.72 (0.20), residues: 643 sheet: -1.77 (0.65), residues: 57 loop : -1.91 (0.31), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.233 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 outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1989 time to fit residues: 64.6839 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.0020 chunk 34 optimal weight: 0.7980 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.171 Angle : 0.700 8.668 12160 Z= 0.342 Chirality : 0.045 0.217 1327 Planarity : 0.004 0.042 1549 Dihedral : 6.503 59.305 1204 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.59 (0.25), residues: 1065 helix: -0.46 (0.20), residues: 646 sheet: -1.66 (0.68), residues: 51 loop : -1.88 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 1.147 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 outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2098 time to fit residues: 70.3687 Evaluate side-chains 191 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 212 HIS B 478 ASN B 736 GLN B 739 ASN ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9008 Z= 0.274 Angle : 0.774 10.399 12160 Z= 0.392 Chirality : 0.049 0.253 1327 Planarity : 0.004 0.034 1549 Dihedral : 6.669 59.403 1204 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.58 (0.25), residues: 1065 helix: -0.47 (0.20), residues: 645 sheet: -1.51 (0.72), residues: 51 loop : -1.84 (0.30), residues: 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.406 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 outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2334 time to fit residues: 78.8190 Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS B 478 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9008 Z= 0.261 Angle : 0.773 8.393 12160 Z= 0.392 Chirality : 0.049 0.253 1327 Planarity : 0.004 0.041 1549 Dihedral : 6.745 57.968 1204 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.48 (0.25), residues: 1065 helix: -0.39 (0.20), residues: 636 sheet: -1.53 (0.70), residues: 53 loop : -1.77 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2133 time to fit residues: 69.8200 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.0030 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 0.0770 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.173 Angle : 0.720 8.556 12160 Z= 0.355 Chirality : 0.046 0.216 1327 Planarity : 0.004 0.044 1549 Dihedral : 6.442 57.068 1204 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.15 (0.25), residues: 1065 helix: -0.12 (0.20), residues: 635 sheet: -1.37 (0.70), residues: 53 loop : -1.66 (0.32), residues: 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2192 time to fit residues: 74.4585 Evaluate side-chains 190 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9008 Z= 0.197 Angle : 0.744 8.845 12160 Z= 0.369 Chirality : 0.047 0.229 1327 Planarity : 0.004 0.044 1549 Dihedral : 6.417 58.298 1204 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1065 helix: -0.07 (0.20), residues: 634 sheet: -1.36 (0.71), residues: 53 loop : -1.58 (0.32), residues: 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2045 time to fit residues: 66.1240 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.191 Angle : 0.730 8.835 12160 Z= 0.363 Chirality : 0.046 0.241 1327 Planarity : 0.004 0.044 1549 Dihedral : 6.416 58.373 1204 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.08 (0.25), residues: 1065 helix: -0.11 (0.20), residues: 634 sheet: -1.26 (0.72), residues: 53 loop : -1.54 (0.32), residues: 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.051 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 outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.2011 time to fit residues: 64.3314 Evaluate side-chains 177 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.137310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111561 restraints weight = 20022.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114087 restraints weight = 12481.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115877 restraints weight = 9038.430| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9008 Z= 0.241 Angle : 0.772 9.965 12160 Z= 0.388 Chirality : 0.049 0.247 1327 Planarity : 0.004 0.041 1549 Dihedral : 6.574 59.977 1204 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.18 (0.25), residues: 1065 helix: -0.15 (0.20), residues: 631 sheet: -1.34 (0.74), residues: 53 loop : -1.63 (0.31), residues: 381 =============================================================================== Job complete usr+sys time: 2091.64 seconds wall clock time: 38 minutes 40.87 seconds (2320.87 seconds total)