Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:14:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/04_2023/6pw9_20501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/04_2023/6pw9_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_20501/04_2023/6pw9_20501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/04_2023/6pw9_20501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/04_2023/6pw9_20501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/04_2023/6pw9_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 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. 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-1.21rc1-4938/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: 5.41, per 1000 atoms: 0.61 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: 3.49 Conformation dependent library (CDL) restraints added in 1.4 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: 0.87 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: 2.39 Time building geometry restraints manager: 3.78 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 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: 1.230 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: 2.790 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.780 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 : 6.70 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 : 1.204 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: 0.2743 time to fit residues: 113.7875 Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1627 time to fit residues: 2.7137 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.6980 chunk 96 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7091 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9008 Z= 0.173 Angle : 0.727 9.864 12160 Z= 0.358 Chirality : 0.046 0.317 1327 Planarity : 0.005 0.066 1549 Dihedral : 7.088 58.402 1204 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.85 % 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: -2.81 (0.23), residues: 1065 helix: -1.47 (0.19), residues: 642 sheet: -2.07 (0.58), residues: 62 loop : -2.29 (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 261 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 253 time to evaluate : 1.120 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: 8 outliers final: 2 residues processed: 259 average time/residue: 0.2363 time to fit residues: 82.3392 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0925 time to fit residues: 1.8003 ------------------------------------------------------------------------------- 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: 0.0980 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 509 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9008 Z= 0.209 Angle : 0.718 8.818 12160 Z= 0.358 Chirality : 0.046 0.249 1327 Planarity : 0.004 0.044 1549 Dihedral : 6.830 59.501 1204 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -2.21 (0.24), residues: 1065 helix: -0.96 (0.20), residues: 647 sheet: -1.79 (0.61), residues: 67 loop : -2.12 (0.30), residues: 351 *********************** 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 241 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 1.159 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: 2 outliers final: 1 residues processed: 241 average time/residue: 0.2284 time to fit residues: 74.8530 Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0867 time to fit residues: 1.6989 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 95 HIS A 148 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 9008 Z= 0.326 Angle : 0.841 9.049 12160 Z= 0.433 Chirality : 0.052 0.276 1327 Planarity : 0.005 0.047 1549 Dihedral : 7.080 57.954 1204 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1065 helix: -1.02 (0.19), residues: 644 sheet: -0.90 (0.86), residues: 36 loop : -2.16 (0.29), residues: 385 *********************** 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 236 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.149 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: 3 outliers final: 1 residues processed: 235 average time/residue: 0.2237 time to fit residues: 71.5904 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0852 time to fit residues: 1.6936 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 736 GLN B 739 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9008 Z= 0.205 Angle : 0.730 8.685 12160 Z= 0.366 Chirality : 0.047 0.241 1327 Planarity : 0.004 0.062 1549 Dihedral : 6.781 57.306 1204 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: -1.76 (0.25), residues: 1065 helix: -0.57 (0.20), residues: 638 sheet: -1.26 (0.77), residues: 48 loop : -2.05 (0.30), residues: 379 *********************** 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 241 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.090 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: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2203 time to fit residues: 72.1042 Evaluate side-chains 189 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4207 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** 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 71 HIS C 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 9008 Z= 0.255 Angle : 0.773 8.458 12160 Z= 0.392 Chirality : 0.048 0.263 1327 Planarity : 0.004 0.034 1549 Dihedral : 6.835 56.442 1204 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: -1.73 (0.25), residues: 1065 helix: -0.54 (0.20), residues: 640 sheet: -1.94 (0.65), residues: 62 loop : -1.93 (0.31), residues: 363 *********************** 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 234 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.113 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: 234 average time/residue: 0.2249 time to fit residues: 72.6627 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4964 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN ** 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: 0.7391 moved from start: 0.5248 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= 0.201 Angle : 0.747 8.711 12160 Z= 0.374 Chirality : 0.047 0.247 1327 Planarity : 0.004 0.040 1549 Dihedral : 6.695 55.819 1204 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -1.46 (0.25), residues: 1065 helix: -0.32 (0.20), residues: 640 sheet: -1.45 (0.77), residues: 48 loop : -1.90 (0.31), residues: 377 *********************** 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 233 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.079 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: 233 average time/residue: 0.2199 time to fit residues: 71.4003 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5421 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 89 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 148 HIS B 124 GLN B 159 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5296 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 : 0.729 9.230 12160 Z= 0.357 Chirality : 0.046 0.226 1327 Planarity : 0.004 0.044 1549 Dihedral : 6.484 55.803 1204 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -1.13 (0.25), residues: 1065 helix: -0.06 (0.20), residues: 638 sheet: -1.49 (0.68), residues: 57 loop : -1.73 (0.32), residues: 370 *********************** 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 236 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.183 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: 236 average time/residue: 0.2117 time to fit residues: 70.3287 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4308 ------------------------------------------------------------------------------- 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: 0.7980 chunk 97 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5376 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= 0.176 Angle : 0.733 8.284 12160 Z= 0.362 Chirality : 0.046 0.228 1327 Planarity : 0.004 0.047 1549 Dihedral : 6.411 55.618 1204 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -1.05 (0.25), residues: 1065 helix: 0.00 (0.20), residues: 644 sheet: -1.28 (0.74), residues: 48 loop : -1.74 (0.31), residues: 373 *********************** 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 232 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2025 time to fit residues: 65.8805 Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5344 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 B 159 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 526 HIS ** 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: 0.7373 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9008 Z= 0.229 Angle : 0.764 10.610 12160 Z= 0.384 Chirality : 0.048 0.242 1327 Planarity : 0.004 0.046 1549 Dihedral : 6.460 56.393 1204 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -1.06 (0.25), residues: 1065 helix: -0.01 (0.20), residues: 634 sheet: -1.59 (0.69), residues: 53 loop : -1.64 (0.31), 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 219 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.084 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: 219 average time/residue: 0.2156 time to fit residues: 66.3888 Evaluate side-chains 176 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5443 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 0.0020 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.141901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116209 restraints weight = 19696.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119054 restraints weight = 11869.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121003 restraints weight = 8366.488| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5600 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= 0.174 Angle : 0.736 9.427 12160 Z= 0.361 Chirality : 0.045 0.217 1327 Planarity : 0.004 0.049 1549 Dihedral : 6.331 55.778 1204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -0.96 (0.25), residues: 1065 helix: 0.10 (0.21), residues: 637 sheet: -1.41 (0.70), residues: 53 loop : -1.68 (0.31), residues: 375 =============================================================================== Job complete usr+sys time: 2068.32 seconds wall clock time: 38 minutes 26.86 seconds (2306.86 seconds total)