Starting phenix.real_space_refine (version: dev) on Fri May 13 03:04:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/05_2022/6hd5_0201_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 "t PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 9707 Number of models: 1 Model: "" Number of chains: 3 Chain: "t" Number of atoms: 6650 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 838, 6650 Classifications: {'peptide': 838} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 27, 'TRANS': 810} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "u" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1798 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 227} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "v" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1259 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PHE v 36 " occ=0.79 ... (9 atoms not shown) pdb=" CZ PHE v 36 " occ=0.79 Time building chain proxies: 5.92, per 1000 atoms: 0.61 Number of scatterers: 9707 At special positions: 0 Unit cell: (123.576, 110.568, 113.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1817 8.00 N 1643 7.00 C 6209 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 61.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 't' and resid 18 through 33 removed outlier: 3.564A pdb=" N ASP t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS t 29 " --> pdb=" O LEU t 25 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 36 through 50 removed outlier: 3.768A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 68 removed outlier: 3.569A pdb=" N GLY t 68 " --> pdb=" O LEU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 83 Processing helix chain 't' and resid 90 through 104 removed outlier: 3.722A pdb=" N CYS t 94 " --> pdb=" O SER t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 107 through 122 removed outlier: 3.587A pdb=" N GLY t 121 " --> pdb=" O ALA t 117 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER t 122 " --> pdb=" O LEU t 118 " (cutoff:3.500A) Processing helix chain 't' and resid 125 through 139 removed outlier: 3.771A pdb=" N ARG t 129 " --> pdb=" O LYS t 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER t 136 " --> pdb=" O ALA t 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE t 138 " --> pdb=" O LEU t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 141 through 155 removed outlier: 3.866A pdb=" N VAL t 146 " --> pdb=" O LYS t 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE t 155 " --> pdb=" O TYR t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 158 through 173 removed outlier: 3.966A pdb=" N TRP t 162 " --> pdb=" O TYR t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 174 through 189 Processing helix chain 't' and resid 195 through 215 removed outlier: 4.328A pdb=" N TYR t 199 " --> pdb=" O ASP t 195 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU t 200 " --> pdb=" O SER t 196 " (cutoff:3.500A) Processing helix chain 't' and resid 219 through 234 Processing helix chain 't' and resid 240 through 255 Processing helix chain 't' and resid 256 through 271 removed outlier: 3.764A pdb=" N ALA t 260 " --> pdb=" O GLN t 256 " (cutoff:3.500A) Processing helix chain 't' and resid 274 through 286 removed outlier: 3.579A pdb=" N TYR t 278 " --> pdb=" O ASN t 274 " (cutoff:3.500A) Processing helix chain 't' and resid 290 through 303 removed outlier: 3.989A pdb=" N LYS t 294 " --> pdb=" O ASP t 290 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN t 303 " --> pdb=" O GLY t 299 " (cutoff:3.500A) Processing helix chain 't' and resid 309 through 314 Processing helix chain 't' and resid 315 through 318 removed outlier: 3.904A pdb=" N PHE t 318 " --> pdb=" O PRO t 315 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 315 through 318' Processing helix chain 't' and resid 321 through 340 Proline residue: t 335 - end of helix Processing helix chain 't' and resid 343 through 348 Processing helix chain 't' and resid 348 through 355 Processing helix chain 't' and resid 359 through 372 Processing helix chain 't' and resid 379 through 397 Processing helix chain 't' and resid 400 through 414 Processing helix chain 't' and resid 417 through 431 removed outlier: 3.878A pdb=" N TYR t 421 " --> pdb=" O LEU t 417 " (cutoff:3.500A) Processing helix chain 't' and resid 433 through 446 Processing helix chain 't' and resid 452 through 464 Processing helix chain 't' and resid 468 through 476 Processing helix chain 't' and resid 487 through 494 Processing helix chain 't' and resid 497 through 525 removed outlier: 3.700A pdb=" N LYS t 515 " --> pdb=" O TYR t 511 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS t 516 " --> pdb=" O LEU t 512 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU t 524 " --> pdb=" O ASP t 520 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS t 525 " --> pdb=" O LEU t 521 " (cutoff:3.500A) Processing helix chain 't' and resid 531 through 536 removed outlier: 3.554A pdb=" N ILE t 536 " --> pdb=" O LYS t 532 " (cutoff:3.500A) Processing helix chain 't' and resid 537 through 559 removed outlier: 3.529A pdb=" N ASN t 559 " --> pdb=" O LEU t 555 " (cutoff:3.500A) Processing helix chain 't' and resid 560 through 571 Processing helix chain 't' and resid 574 through 582 removed outlier: 4.099A pdb=" N MET t 580 " --> pdb=" O HIS t 576 " (cutoff:3.500A) Processing helix chain 't' and resid 584 through 598 Processing helix chain 't' and resid 601 through 627 removed outlier: 4.351A pdb=" N SER t 627 " --> pdb=" O LEU t 623 " (cutoff:3.500A) Processing helix chain 't' and resid 646 through 669 Processing helix chain 't' and resid 690 through 699 Processing helix chain 't' and resid 700 through 706 Processing helix chain 't' and resid 713 through 723 removed outlier: 3.596A pdb=" N ASP t 717 " --> pdb=" O ASP t 713 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG t 723 " --> pdb=" O GLU t 719 " (cutoff:3.500A) Processing helix chain 't' and resid 727 through 741 Processing helix chain 't' and resid 745 through 759 removed outlier: 3.593A pdb=" N GLY t 749 " --> pdb=" O SER t 745 " (cutoff:3.500A) Processing helix chain 't' and resid 766 through 781 Processing helix chain 't' and resid 796 through 805 removed outlier: 3.847A pdb=" N PHE t 800 " --> pdb=" O ASP t 796 " (cutoff:3.500A) Processing helix chain 't' and resid 810 through 819 Processing helix chain 't' and resid 827 through 838 Processing helix chain 't' and resid 842 through 852 Processing helix chain 'u' and resid 9 through 11 No H-bonds generated for 'chain 'u' and resid 9 through 11' Processing helix chain 'u' and resid 12 through 22 Processing helix chain 'u' and resid 29 through 39 removed outlier: 3.536A pdb=" N TYR u 33 " --> pdb=" O MET u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 129 through 145 Processing helix chain 'u' and resid 158 through 166 Processing helix chain 'u' and resid 201 through 205 removed outlier: 3.973A pdb=" N THR u 205 " --> pdb=" O SER u 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 23 removed outlier: 3.678A pdb=" N LEU v 19 " --> pdb=" O ASN v 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA v 23 " --> pdb=" O LEU v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 38 Processing helix chain 'v' and resid 106 through 122 Processing helix chain 'v' and resid 136 through 147 removed outlier: 3.705A pdb=" N HIS v 145 " --> pdb=" O TRP v 141 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY v 146 " --> pdb=" O PHE v 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE v 147 " --> pdb=" O ILE v 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'u' and resid 4 through 7 removed outlier: 6.639A pdb=" N GLU u 90 " --> pdb=" O LEU u 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'u' and resid 4 through 7 removed outlier: 6.426A pdb=" N LYS u 99 " --> pdb=" O ILE u 115 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE u 115 " --> pdb=" O LYS u 99 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS u 153 " --> pdb=" O ILE u 115 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER u 117 " --> pdb=" O HIS u 153 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS u 191 " --> pdb=" O VAL u 173 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL u 173 " --> pdb=" O LYS u 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'v' and resid 6 through 9 removed outlier: 4.073A pdb=" N VAL v 58 " --> pdb=" O LEU v 78 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR v 66 " --> pdb=" O PRO v 70 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL v 71 " --> pdb=" O VAL v 98 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL v 98 " --> pdb=" O VAL v 71 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY v 73 " --> pdb=" O LEU v 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU v 96 " --> pdb=" O GLY v 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL v 75 " --> pdb=" O GLU v 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE v 128 " --> pdb=" O ILE v 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE v 93 " --> pdb=" O PHE v 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR v 130 " --> pdb=" O ILE v 93 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE v 95 " --> pdb=" O TYR v 130 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N GLY v 97 " --> pdb=" O PRO v 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'v' and resid 6 through 9 removed outlier: 4.073A pdb=" N VAL v 58 " --> pdb=" O LEU v 78 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR v 66 " --> pdb=" O PRO v 70 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL v 71 " --> pdb=" O VAL v 98 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL v 98 " --> pdb=" O VAL v 71 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY v 73 " --> pdb=" O LEU v 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU v 96 " --> pdb=" O GLY v 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL v 75 " --> pdb=" O GLU v 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE v 128 " --> pdb=" O ILE v 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE v 93 " --> pdb=" O PHE v 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR v 130 " --> pdb=" O ILE v 93 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE v 95 " --> pdb=" O TYR v 130 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N GLY v 97 " --> pdb=" O PRO v 132 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN v 166 " --> pdb=" O PHE v 157 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA v 168 " --> pdb=" O ASN v 155 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN v 155 " --> pdb=" O ALA v 168 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1679 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: 3.18 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3177 1.34 - 1.46: 1705 1.46 - 1.58: 4964 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9909 Sorted by residual: bond pdb=" CA ASN t 639 " pdb=" C ASN t 639 " ideal model delta sigma weight residual 1.531 1.523 0.007 5.40e-03 3.43e+04 1.90e+00 bond pdb=" N GLY t 86 " pdb=" CA GLY t 86 " ideal model delta sigma weight residual 1.444 1.455 -0.011 9.60e-03 1.09e+04 1.31e+00 bond pdb=" CA GLU t 495 " pdb=" C GLU t 495 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.70e-01 bond pdb=" C GLN t 638 " pdb=" N ASN t 639 " ideal model delta sigma weight residual 1.325 1.333 -0.008 9.70e-03 1.06e+04 7.18e-01 bond pdb=" N ILE v 69 " pdb=" CA ILE v 69 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.16e-01 ... (remaining 9904 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.41: 266 107.41 - 114.05: 5531 114.05 - 120.69: 4460 120.69 - 127.33: 3072 127.33 - 133.97: 81 Bond angle restraints: 13410 Sorted by residual: angle pdb=" C ASN t 643 " pdb=" CA ASN t 643 " pdb=" CB ASN t 643 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" C ASN t 639 " pdb=" CA ASN t 639 " pdb=" CB ASN t 639 " ideal model delta sigma weight residual 116.53 110.54 5.99 1.47e+00 4.63e-01 1.66e+01 angle pdb=" CA ASN t 643 " pdb=" C ASN t 643 " pdb=" N SER t 644 " ideal model delta sigma weight residual 119.98 116.92 3.06 8.50e-01 1.38e+00 1.29e+01 angle pdb=" CA ASN t 639 " pdb=" C ASN t 639 " pdb=" O ASN t 639 " ideal model delta sigma weight residual 118.33 120.33 -2.00 6.30e-01 2.52e+00 1.01e+01 angle pdb=" N LEU u 86 " pdb=" CA LEU u 86 " pdb=" C LEU u 86 " ideal model delta sigma weight residual 114.04 110.24 3.80 1.24e+00 6.50e-01 9.38e+00 ... (remaining 13405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 5748 15.08 - 30.15: 180 30.15 - 45.23: 57 45.23 - 60.31: 0 60.31 - 75.39: 5 Dihedral angle restraints: 5990 sinusoidal: 2331 harmonic: 3659 Sorted by residual: dihedral pdb=" CB LYS t 601 " pdb=" CG LYS t 601 " pdb=" CD LYS t 601 " pdb=" CE LYS t 601 " ideal model delta sinusoidal sigma weight residual 60.00 103.00 -43.00 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LYS t 29 " pdb=" CB LYS t 29 " pdb=" CG LYS t 29 " pdb=" CD LYS t 29 " ideal model delta sinusoidal sigma weight residual 60.00 100.75 -40.75 3 1.50e+01 4.44e-03 7.27e+00 dihedral pdb=" CA LYS t 551 " pdb=" CB LYS t 551 " pdb=" CG LYS t 551 " pdb=" CD LYS t 551 " ideal model delta sinusoidal sigma weight residual -60.00 -98.67 38.67 3 1.50e+01 4.44e-03 6.82e+00 ... (remaining 5987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 956 0.025 - 0.050: 327 0.050 - 0.075: 125 0.075 - 0.100: 51 0.100 - 0.125: 20 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA ILE u 5 " pdb=" N ILE u 5 " pdb=" C ILE u 5 " pdb=" CB ILE u 5 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE u 176 " pdb=" N ILE u 176 " pdb=" C ILE u 176 " pdb=" CB ILE u 176 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA VAL v 98 " pdb=" N VAL v 98 " pdb=" C VAL v 98 " pdb=" CB VAL v 98 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 1476 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL t 341 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO t 342 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO t 342 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO t 342 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER t 839 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO t 840 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO t 840 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO t 840 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU t 309 " 0.026 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO t 310 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO t 310 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO t 310 " 0.021 5.00e-02 4.00e+02 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2708 2.81 - 3.33: 9007 3.33 - 3.86: 15498 3.86 - 4.38: 16644 4.38 - 4.90: 30197 Nonbonded interactions: 74054 Sorted by model distance: nonbonded pdb=" OE2 GLU u 109 " pdb=" OH TYR u 149 " model vdw 2.289 2.440 nonbonded pdb=" OE1 GLU t 842 " pdb=" NE2 HIS t 844 " model vdw 2.295 2.520 nonbonded pdb=" O LYS t 356 " pdb=" OG SER t 360 " model vdw 2.324 2.440 nonbonded pdb=" OD2 ASP t 375 " pdb=" OG1 THR t 377 " model vdw 2.334 2.440 nonbonded pdb=" O LYS t 19 " pdb=" NE2 GLN t 23 " model vdw 2.345 2.520 ... (remaining 74049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6209 2.51 5 N 1643 2.21 5 O 1817 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=0.77 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 15.760 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 29.430 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3180 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 : 0.001 0.022 9909 Z= 0.087 Angle : 0.403 6.837 13410 Z= 0.249 Chirality : 0.034 0.125 1479 Planarity : 0.003 0.040 1735 Dihedral : 8.701 75.387 3626 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.52 % Favored : 88.42 % Rotamer Outliers : 0.10 % 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: -1.81 (0.22), residues: 1226 helix: 0.03 (0.18), residues: 745 sheet: -1.69 (0.56), residues: 72 loop : -3.45 (0.25), residues: 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.089 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: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2660 time to fit residues: 110.5087 Evaluate side-chains 163 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 62 optimal weight: 0.0060 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 161 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 180 ASN ** t 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 320 GLN ** t 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 492 HIS t 543 ASN t 701 ASN t 735 ASN u 20 ASN ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 HIS u 153 HIS v 32 GLN v 59 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3837 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9909 Z= 0.239 Angle : 0.666 8.941 13410 Z= 0.340 Chirality : 0.041 0.159 1479 Planarity : 0.005 0.090 1735 Dihedral : 3.729 25.322 1346 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer Outliers : 0.10 % 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: -0.66 (0.23), residues: 1226 helix: 0.96 (0.19), residues: 732 sheet: -0.61 (0.58), residues: 81 loop : -3.09 (0.26), residues: 413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2285 time to fit residues: 66.8270 Evaluate side-chains 150 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 109 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 119 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 ASN t 347 ASN t 572 GLN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3952 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9909 Z= 0.184 Angle : 0.569 7.107 13410 Z= 0.291 Chirality : 0.038 0.122 1479 Planarity : 0.004 0.063 1735 Dihedral : 3.578 25.114 1346 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.55 % Favored : 94.21 % Rotamer Outliers : 0.10 % 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: -0.23 (0.24), residues: 1226 helix: 1.29 (0.19), residues: 738 sheet: -0.37 (0.59), residues: 81 loop : -2.96 (0.26), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2253 time to fit residues: 60.1835 Evaluate side-chains 140 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 0.0980 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 143 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 392 GLN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4010 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 9909 Z= 0.190 Angle : 0.577 6.845 13410 Z= 0.293 Chirality : 0.039 0.303 1479 Planarity : 0.004 0.099 1735 Dihedral : 3.635 24.834 1346 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer Outliers : 0.10 % 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: -0.11 (0.24), residues: 1226 helix: 1.30 (0.19), residues: 753 sheet: -0.23 (0.58), residues: 81 loop : -2.92 (0.28), residues: 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2132 time to fit residues: 55.0953 Evaluate side-chains 134 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.0170 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 3.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 172 ASN t 219 ASN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 GLN ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4073 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9909 Z= 0.184 Angle : 0.571 7.111 13410 Z= 0.291 Chirality : 0.039 0.219 1479 Planarity : 0.004 0.072 1735 Dihedral : 3.705 24.226 1346 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.87 % Favored : 93.88 % Rotamer Outliers : 0.10 % 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: 0.00 (0.25), residues: 1226 helix: 1.39 (0.19), residues: 750 sheet: -0.24 (0.59), residues: 81 loop : -2.81 (0.28), residues: 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2158 time to fit residues: 55.2435 Evaluate side-chains 134 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 103 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 544 GLN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 676 GLN t 847 ASN ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4314 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9909 Z= 0.246 Angle : 0.660 7.164 13410 Z= 0.339 Chirality : 0.040 0.215 1479 Planarity : 0.004 0.061 1735 Dihedral : 4.163 22.837 1346 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.79 % Favored : 93.96 % 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: -0.36 (0.24), residues: 1226 helix: 1.07 (0.19), residues: 748 sheet: -0.48 (0.55), residues: 81 loop : -2.83 (0.28), residues: 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.131 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: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2031 time to fit residues: 49.2406 Evaluate side-chains 124 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 53 HIS t 119 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 619 HIS t 735 ASN ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4223 moved from start: 0.7073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9909 Z= 0.171 Angle : 0.593 7.408 13410 Z= 0.300 Chirality : 0.039 0.178 1479 Planarity : 0.004 0.053 1735 Dihedral : 3.947 23.272 1346 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % 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: -0.14 (0.24), residues: 1226 helix: 1.28 (0.19), residues: 742 sheet: -0.37 (0.55), residues: 84 loop : -2.78 (0.28), residues: 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2214 time to fit residues: 52.8194 Evaluate side-chains 123 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 119 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.111 9909 Z= 0.238 Angle : 0.661 7.898 13410 Z= 0.338 Chirality : 0.041 0.185 1479 Planarity : 0.006 0.130 1735 Dihedral : 4.152 22.639 1346 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % 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: -0.31 (0.24), residues: 1226 helix: 1.14 (0.19), residues: 739 sheet: -0.48 (0.57), residues: 79 loop : -2.78 (0.28), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.151 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: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2201 time to fit residues: 49.9803 Evaluate side-chains 117 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0050 chunk 102 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 2.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 53 HIS ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4268 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 9909 Z= 0.186 Angle : 0.625 8.869 13410 Z= 0.314 Chirality : 0.040 0.174 1479 Planarity : 0.005 0.109 1735 Dihedral : 4.068 22.556 1346 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.05 % 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: -0.22 (0.24), residues: 1226 helix: 1.19 (0.19), residues: 747 sheet: -0.47 (0.59), residues: 76 loop : -2.75 (0.28), residues: 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2166 time to fit residues: 50.1258 Evaluate side-chains 117 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4332 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 9909 Z= 0.206 Angle : 0.647 8.551 13410 Z= 0.329 Chirality : 0.041 0.234 1479 Planarity : 0.005 0.103 1735 Dihedral : 4.119 21.750 1346 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.36 % Favored : 93.47 % 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: -0.21 (0.24), residues: 1226 helix: 1.16 (0.19), residues: 741 sheet: -0.38 (0.59), residues: 76 loop : -2.63 (0.28), residues: 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2135 time to fit residues: 49.3853 Evaluate side-chains 119 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.0898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 20 ASN ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.224158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.208569 restraints weight = 53931.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.210260 restraints weight = 38119.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.211495 restraints weight = 27603.339| |-----------------------------------------------------------------------------| r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5137 r_free = 0.5137 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5134 r_free = 0.5134 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.5134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 9909 Z= 0.179 Angle : 0.625 8.203 13410 Z= 0.313 Chirality : 0.040 0.257 1479 Planarity : 0.004 0.096 1735 Dihedral : 3.972 21.479 1346 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % 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: -0.09 (0.24), residues: 1226 helix: 1.28 (0.19), residues: 748 sheet: -0.29 (0.61), residues: 76 loop : -2.71 (0.27), residues: 402 =============================================================================== Job complete usr+sys time: 2047.04 seconds wall clock time: 38 minutes 13.63 seconds (2293.63 seconds total)