Starting phenix.real_space_refine on Sat Dec 9 01:59:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/12_2023/6hd5_0201_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/12_2023/6hd5_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_0201/12_2023/6hd5_0201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/12_2023/6hd5_0201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/12_2023/6hd5_0201_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/12_2023/6hd5_0201_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.48, per 1000 atoms: 0.56 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: 3.82 Conformation dependent library (CDL) restraints added in 1.6 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: 1.15 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: 2.93 Time building geometry restraints manager: 4.15 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 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: 3.280 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: 15.310 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 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 : 4.36 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.52 % Favored : 88.42 % Rotamer: Outliers : 0.10 % Allowed : 1.01 % Favored : 98.89 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP t 385 HIS 0.002 0.000 HIS t 576 PHE 0.007 0.000 PHE t 800 TYR 0.012 0.001 TYR t 507 ARG 0.001 0.000 ARG u 142 *********************** 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 : 1.146 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 outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2872 time to fit residues: 119.0882 Evaluate side-chains 164 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5981 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3974 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9909 Z= 0.239 Angle : 0.659 8.771 13410 Z= 0.336 Chirality : 0.040 0.164 1479 Planarity : 0.004 0.046 1735 Dihedral : 3.664 24.715 1346 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.68 % 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: -0.63 (0.23), residues: 1226 helix: 1.01 (0.19), residues: 731 sheet: -0.64 (0.57), residues: 81 loop : -3.11 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP t 162 HIS 0.008 0.002 HIS v 59 PHE 0.018 0.002 PHE t 400 TYR 0.030 0.002 TYR t 199 ARG 0.006 0.001 ARG t 270 *********************** 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 214 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.037 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: 213 average time/residue: 0.2330 time to fit residues: 68.3075 Evaluate side-chains 151 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5562 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 109 optimal weight: 0.0970 overall best weight: 5.4186 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 572 GLN ** u 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4232 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9909 Z= 0.233 Angle : 0.629 6.528 13410 Z= 0.328 Chirality : 0.039 0.147 1479 Planarity : 0.004 0.070 1735 Dihedral : 3.821 24.357 1346 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.20 % Favored : 93.56 % Rotamer: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % 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: -0.41 (0.24), residues: 1226 helix: 1.08 (0.19), residues: 746 sheet: -0.54 (0.57), residues: 81 loop : -2.94 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP t 797 HIS 0.005 0.001 HIS v 59 PHE 0.021 0.002 PHE u 139 TYR 0.055 0.002 TYR t 550 ARG 0.006 0.001 ARG u 125 *********************** 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 194 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.132 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 outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2197 time to fit residues: 59.5152 Evaluate side-chains 139 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4604 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 0.1980 chunk 111 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 23 GLN t 119 ASN t 143 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 ASN t 347 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 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4202 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9909 Z= 0.176 Angle : 0.571 7.511 13410 Z= 0.291 Chirality : 0.039 0.274 1479 Planarity : 0.003 0.035 1735 Dihedral : 3.705 24.352 1346 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -0.12 (0.24), residues: 1226 helix: 1.29 (0.19), residues: 747 sheet: -0.27 (0.59), residues: 81 loop : -2.81 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP t 162 HIS 0.004 0.001 HIS t 430 PHE 0.031 0.002 PHE v 114 TYR 0.025 0.001 TYR t 550 ARG 0.005 0.001 ARG u 135 *********************** 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 179 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.083 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 outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2190 time to fit residues: 55.7819 Evaluate side-chains 133 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7244 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 8.9990 chunk 87 optimal weight: 50.0000 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 219 ASN t 481 ASN t 544 GLN 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 136 GLN ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4520 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9909 Z= 0.274 Angle : 0.702 9.369 13410 Z= 0.361 Chirality : 0.042 0.280 1479 Planarity : 0.005 0.041 1735 Dihedral : 4.356 23.052 1346 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.20 % Favored : 93.56 % Rotamer: Outliers : 0.30 % Allowed : 2.42 % Favored : 97.28 % 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: -0.56 (0.24), residues: 1226 helix: 0.92 (0.19), residues: 748 sheet: -0.71 (0.55), residues: 81 loop : -2.88 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP t 152 HIS 0.005 0.002 HIS u 206 PHE 0.038 0.003 PHE u 45 TYR 0.028 0.002 TYR t 550 ARG 0.026 0.001 ARG t 557 *********************** 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 169 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.045 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: 3 outliers final: 0 residues processed: 168 average time/residue: 0.2130 time to fit residues: 50.9287 Evaluate side-chains 126 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5783 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 172 ASN ** t 209 ASN ** 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** u 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4410 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9909 Z= 0.192 Angle : 0.611 7.463 13410 Z= 0.309 Chirality : 0.040 0.195 1479 Planarity : 0.004 0.051 1735 Dihedral : 4.132 24.035 1346 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -0.27 (0.24), residues: 1226 helix: 1.18 (0.19), residues: 742 sheet: -0.77 (0.57), residues: 76 loop : -2.71 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 162 HIS 0.003 0.001 HIS t 430 PHE 0.028 0.002 PHE u 45 TYR 0.022 0.001 TYR t 550 ARG 0.014 0.001 ARG t 557 *********************** 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 168 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.126 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: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2418 time to fit residues: 57.2116 Evaluate side-chains 128 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6643 ------------------------------------------------------------------------------- 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: 0.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 ASN ** 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** u 136 GLN u 153 HIS ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4609 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9909 Z= 0.233 Angle : 0.678 7.601 13410 Z= 0.349 Chirality : 0.040 0.140 1479 Planarity : 0.005 0.060 1735 Dihedral : 4.438 23.197 1346 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.04 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -0.62 (0.24), residues: 1226 helix: 0.92 (0.19), residues: 747 sheet: -1.05 (0.54), residues: 76 loop : -2.92 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP t 385 HIS 0.006 0.001 HIS u 206 PHE 0.029 0.002 PHE u 45 TYR 0.025 0.002 TYR t 700 ARG 0.008 0.001 ARG t 557 *********************** 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 : 1.083 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: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2369 time to fit residues: 54.9622 Evaluate side-chains 129 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5337 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 481 ASN ** 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** u 136 GLN ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4579 moved from start: 0.7983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9909 Z= 0.191 Angle : 0.642 7.757 13410 Z= 0.327 Chirality : 0.040 0.182 1479 Planarity : 0.005 0.093 1735 Dihedral : 4.410 23.651 1346 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -0.54 (0.24), residues: 1226 helix: 0.98 (0.19), residues: 744 sheet: -1.34 (0.52), residues: 83 loop : -2.80 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP t 162 HIS 0.008 0.001 HIS t 53 PHE 0.027 0.002 PHE u 45 TYR 0.031 0.002 TYR t 700 ARG 0.010 0.001 ARG u 155 *********************** 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 170 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.209 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: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2478 time to fit residues: 58.1557 Evaluate side-chains 131 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5596 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 65 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 119 ASN ** t 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** 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** u 136 GLN ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4470 moved from start: 0.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9909 Z= 0.178 Angle : 0.639 9.157 13410 Z= 0.323 Chirality : 0.040 0.234 1479 Planarity : 0.006 0.220 1735 Dihedral : 4.306 28.601 1346 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 1.11 (0.19), residues: 742 sheet: -1.17 (0.55), residues: 83 loop : -2.69 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP t 162 HIS 0.003 0.001 HIS u 114 PHE 0.021 0.002 PHE u 45 TYR 0.019 0.001 TYR t 550 ARG 0.012 0.001 ARG u 155 *********************** 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 171 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2418 time to fit residues: 57.5247 Evaluate side-chains 131 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4688 ------------------------------------------------------------------------------- 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: 10.0000 chunk 80 optimal weight: 0.0270 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 101 ASN v 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4411 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9909 Z= 0.174 Angle : 0.650 10.987 13410 Z= 0.325 Chirality : 0.041 0.204 1479 Planarity : 0.007 0.198 1735 Dihedral : 4.178 24.780 1346 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1226 helix: 1.11 (0.19), residues: 748 sheet: -0.98 (0.56), residues: 81 loop : -2.69 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP t 162 HIS 0.006 0.001 HIS t 53 PHE 0.019 0.001 PHE u 45 TYR 0.037 0.002 TYR t 700 ARG 0.015 0.001 ARG t 557 ********************** 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 163 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.169 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: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2421 time to fit residues: 54.5497 Evaluate side-chains 140 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5685 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 50.0000 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 735 ASN u 20 ASN ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.215315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.199449 restraints weight = 54418.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.201146 restraints weight = 38120.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.202371 restraints weight = 27859.154| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4563 r_free = 0.4563 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4562 r_free = 0.4562 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.8468 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= 0.227 Angle : 0.696 8.698 13410 Z= 0.356 Chirality : 0.041 0.224 1479 Planarity : 0.007 0.207 1735 Dihedral : 4.538 26.482 1346 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1226 helix: 1.00 (0.19), residues: 741 sheet: -0.98 (0.57), residues: 75 loop : -2.54 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 162 HIS 0.006 0.001 HIS u 206 PHE 0.019 0.002 PHE u 45 TYR 0.047 0.002 TYR t 406 ARG 0.015 0.001 ARG t 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.45 seconds wall clock time: 40 minutes 33.40 seconds (2433.40 seconds total)