Starting phenix.real_space_refine on Thu Mar 14 20:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/03_2024/6hd5_0201_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/03_2024/6hd5_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_0201/03_2024/6hd5_0201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/03_2024/6hd5_0201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/03_2024/6hd5_0201_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd5_0201/03_2024/6hd5_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-dev-5265/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: 3.56 Conformation dependent library (CDL) restraints added in 1.7 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: 1.12 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: 2.70 Time building geometry restraints manager: 3.90 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: 4.330 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: 15.300 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.450 Find NCS groups from input model: 0.240 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- 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 : 1.106 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: t 314 ILE cc_start: 0.7824 (mt) cc_final: 0.7207 (mt) REVERT: t 428 LEU cc_start: 0.8776 (mt) cc_final: 0.8530 (mt) REVERT: t 441 LEU cc_start: 0.7889 (tp) cc_final: 0.7180 (tp) REVERT: t 458 THR cc_start: 0.6485 (m) cc_final: 0.5834 (m) REVERT: t 543 ASN cc_start: 0.5120 (t0) cc_final: 0.4876 (t0) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2821 time to fit residues: 116.2372 Evaluate side-chains 164 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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: 9.9990 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: 5.0004 ------------------------------------------------------------------------------- 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: 0.3973 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9909 Z= 0.233 Angle : 0.656 8.807 13410 Z= 0.334 Chirality : 0.041 0.160 1479 Planarity : 0.004 0.049 1735 Dihedral : 3.647 24.718 1346 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.22 % Favored : 94.54 % Rotamer: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.78 % 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: -0.63 (0.58), residues: 81 loop : -3.11 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP t 162 HIS 0.007 0.001 HIS v 59 PHE 0.018 0.002 PHE t 568 TYR 0.028 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 213 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.998 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: t 314 ILE cc_start: 0.8159 (mt) cc_final: 0.7664 (mt) REVERT: t 441 LEU cc_start: 0.7642 (tp) cc_final: 0.7078 (tp) REVERT: t 458 THR cc_start: 0.6510 (m) cc_final: 0.5790 (m) REVERT: u 49 THR cc_start: 0.6989 (p) cc_final: 0.6690 (p) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2300 time to fit residues: 66.7402 Evaluate side-chains 150 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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: 0.0470 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 109 optimal weight: 3.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- 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 ** t 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 543 ASN ** t 572 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** ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4275 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9909 Z= 0.237 Angle : 0.646 6.739 13410 Z= 0.337 Chirality : 0.040 0.134 1479 Planarity : 0.005 0.074 1735 Dihedral : 3.898 24.309 1346 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 0.10 % Allowed : 2.01 % 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: -0.43 (0.24), residues: 1226 helix: 1.07 (0.19), residues: 744 sheet: -0.49 (0.58), residues: 81 loop : -2.94 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP t 797 HIS 0.006 0.001 HIS v 59 PHE 0.022 0.003 PHE u 139 TYR 0.063 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 192 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.136 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: t 206 MET cc_start: 0.8454 (mtm) cc_final: 0.8212 (mtm) REVERT: t 314 ILE cc_start: 0.8161 (mt) cc_final: 0.7486 (mt) REVERT: t 441 LEU cc_start: 0.7664 (tp) cc_final: 0.7204 (tp) REVERT: t 458 THR cc_start: 0.6506 (m) cc_final: 0.5993 (m) REVERT: t 705 MET cc_start: 0.7663 (ptp) cc_final: 0.7380 (ptp) REVERT: u 10 ILE cc_start: 0.0341 (tt) cc_final: -0.0149 (tt) REVERT: u 115 ILE cc_start: 0.7392 (mm) cc_final: 0.7185 (mm) REVERT: v 65 TYR cc_start: 0.5308 (m-80) cc_final: 0.4826 (m-80) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2101 time to fit residues: 56.7898 Evaluate side-chains 139 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 20.0000 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 172 ASN ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 ASN t 347 ASN t 481 ASN ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9909 Z= 0.226 Angle : 0.629 6.761 13410 Z= 0.324 Chirality : 0.039 0.131 1479 Planarity : 0.004 0.037 1735 Dihedral : 4.028 23.530 1346 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.02 % Rotamer: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.68 % 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: -0.44 (0.24), residues: 1226 helix: 1.02 (0.19), residues: 747 sheet: -0.58 (0.57), residues: 81 loop : -2.86 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP t 162 HIS 0.005 0.001 HIS t 430 PHE 0.026 0.002 PHE u 139 TYR 0.023 0.002 TYR t 550 ARG 0.006 0.001 ARG t 159 *********************** 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: 1 poor density : 178 time to evaluate : 1.128 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: t 206 MET cc_start: 0.8792 (mtm) cc_final: 0.8130 (mtm) REVERT: t 314 ILE cc_start: 0.8171 (mt) cc_final: 0.7563 (mt) REVERT: u 123 THR cc_start: 0.4530 (p) cc_final: 0.4272 (p) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2149 time to fit residues: 54.7056 Evaluate side-chains 128 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 0.0670 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 0.0060 chunk 39 optimal weight: 0.8980 overall best weight: 1.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 53 HIS ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 481 ASN ** t 572 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9909 Z= 0.165 Angle : 0.584 7.375 13410 Z= 0.294 Chirality : 0.039 0.245 1479 Planarity : 0.003 0.037 1735 Dihedral : 3.847 23.820 1346 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.22 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -0.16 (0.24), residues: 1226 helix: 1.23 (0.19), residues: 747 sheet: -0.36 (0.62), residues: 75 loop : -2.72 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP t 162 HIS 0.003 0.001 HIS v 59 PHE 0.035 0.002 PHE u 45 TYR 0.025 0.001 TYR t 550 ARG 0.004 0.000 ARG u 135 *********************** 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 172 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.095 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: t 158 TYR cc_start: 0.5805 (t80) cc_final: 0.4943 (m-80) REVERT: t 206 MET cc_start: 0.8737 (mtm) cc_final: 0.8195 (mtm) REVERT: t 314 ILE cc_start: 0.8121 (mt) cc_final: 0.7435 (mt) REVERT: t 705 MET cc_start: 0.6870 (ptt) cc_final: 0.6392 (ptt) REVERT: t 805 PHE cc_start: 0.5486 (m-80) cc_final: 0.5250 (m-80) REVERT: u 123 THR cc_start: 0.4571 (p) cc_final: 0.4342 (p) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2109 time to fit residues: 51.1749 Evaluate side-chains 130 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 20.0000 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 219 ASN t 544 GLN ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 676 GLN ** 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** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4496 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9909 Z= 0.224 Angle : 0.657 8.401 13410 Z= 0.335 Chirality : 0.041 0.211 1479 Planarity : 0.004 0.039 1735 Dihedral : 4.215 22.646 1346 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.87 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -0.43 (0.24), residues: 1226 helix: 1.00 (0.19), residues: 748 sheet: -0.77 (0.60), residues: 73 loop : -2.71 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP t 162 HIS 0.004 0.001 HIS u 206 PHE 0.036 0.002 PHE u 45 TYR 0.022 0.002 TYR t 550 ARG 0.010 0.001 ARG t 246 *********************** 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 164 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.153 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: t 101 MET cc_start: 0.7401 (ptp) cc_final: 0.6839 (ptm) REVERT: t 158 TYR cc_start: 0.5900 (t80) cc_final: 0.5268 (m-80) REVERT: t 206 MET cc_start: 0.8973 (mtm) cc_final: 0.8325 (mtm) REVERT: t 314 ILE cc_start: 0.8273 (mt) cc_final: 0.7584 (mt) REVERT: t 700 TYR cc_start: 0.3182 (t80) cc_final: 0.2920 (t80) REVERT: t 705 MET cc_start: 0.7118 (ptt) cc_final: 0.6505 (ptt) REVERT: v 128 PHE cc_start: 0.5196 (p90) cc_final: 0.4857 (p90) REVERT: v 172 LYS cc_start: 0.5638 (tppt) cc_final: 0.5106 (tppt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2023 time to fit residues: 47.3028 Evaluate side-chains 124 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 392 GLN ** t 572 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 136 GLN ** u 145 HIS ** 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: 0.4442 moved from start: 0.7355 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= 0.181 Angle : 0.606 9.003 13410 Z= 0.305 Chirality : 0.040 0.193 1479 Planarity : 0.004 0.046 1735 Dihedral : 4.057 22.857 1346 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.45 % 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: -0.28 (0.24), residues: 1226 helix: 1.11 (0.19), residues: 749 sheet: -0.55 (0.60), residues: 76 loop : -2.71 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 152 HIS 0.004 0.001 HIS t 430 PHE 0.029 0.002 PHE u 45 TYR 0.021 0.001 TYR u 181 ARG 0.006 0.001 ARG t 246 *********************** 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 162 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.107 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: t 158 TYR cc_start: 0.5505 (t80) cc_final: 0.5089 (m-80) REVERT: t 206 MET cc_start: 0.8940 (mtm) cc_final: 0.8384 (mtm) REVERT: t 314 ILE cc_start: 0.8130 (mt) cc_final: 0.7469 (mt) REVERT: t 375 ASP cc_start: 0.5105 (t70) cc_final: 0.4856 (t70) REVERT: t 428 LEU cc_start: 0.8440 (mp) cc_final: 0.8225 (mt) REVERT: t 700 TYR cc_start: 0.2862 (t80) cc_final: 0.2521 (t80) REVERT: t 705 MET cc_start: 0.6989 (ptt) cc_final: 0.6426 (ptt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2168 time to fit residues: 49.8346 Evaluate side-chains 126 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 20.0000 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 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 136 GLN ** u 145 HIS ** 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: 0.4500 moved from start: 0.7697 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= 0.195 Angle : 0.638 8.718 13410 Z= 0.323 Chirality : 0.040 0.191 1479 Planarity : 0.004 0.040 1735 Dihedral : 4.147 22.169 1346 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.28 (0.24), residues: 1226 helix: 1.14 (0.19), residues: 749 sheet: -0.56 (0.60), residues: 76 loop : -2.76 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP t 152 HIS 0.004 0.001 HIS u 206 PHE 0.023 0.002 PHE u 45 TYR 0.019 0.001 TYR t 421 ARG 0.006 0.001 ARG t 606 *********************** 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 166 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.003 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: t 158 TYR cc_start: 0.5492 (t80) cc_final: 0.5142 (m-80) REVERT: t 206 MET cc_start: 0.8874 (mtm) cc_final: 0.8198 (mtm) REVERT: t 314 ILE cc_start: 0.8247 (mt) cc_final: 0.7519 (mt) REVERT: t 375 ASP cc_start: 0.5149 (t70) cc_final: 0.4892 (t70) REVERT: t 428 LEU cc_start: 0.8433 (mp) cc_final: 0.8217 (mp) REVERT: t 705 MET cc_start: 0.7027 (ptt) cc_final: 0.6284 (ptt) REVERT: v 172 LYS cc_start: 0.4815 (tppt) cc_final: 0.4479 (tppt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2414 time to fit residues: 55.3961 Evaluate side-chains 123 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 7.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 0.0670 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- 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 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** ** 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: 0.4498 moved from start: 0.7908 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= 0.180 Angle : 0.638 10.680 13410 Z= 0.324 Chirality : 0.040 0.186 1479 Planarity : 0.004 0.040 1735 Dihedral : 4.127 21.867 1346 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -0.19 (0.24), residues: 1226 helix: 1.18 (0.19), residues: 743 sheet: -0.51 (0.60), residues: 76 loop : -2.61 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP t 162 HIS 0.011 0.001 HIS t 53 PHE 0.034 0.002 PHE t 718 TYR 0.018 0.001 TYR t 550 ARG 0.006 0.001 ARG t 606 *********************** 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 : 1.119 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 revert: symmetry clash REVERT: t 108 LYS cc_start: 0.8567 (mppt) cc_final: 0.7999 (mtmt) REVERT: t 206 MET cc_start: 0.8839 (mtm) cc_final: 0.8242 (mtm) REVERT: t 314 ILE cc_start: 0.8194 (mt) cc_final: 0.7605 (mt) REVERT: t 375 ASP cc_start: 0.5275 (t70) cc_final: 0.4983 (t70) REVERT: t 428 LEU cc_start: 0.8439 (mp) cc_final: 0.8225 (mp) REVERT: t 580 MET cc_start: 0.1518 (tpp) cc_final: 0.1117 (tpp) REVERT: t 705 MET cc_start: 0.6879 (ptt) cc_final: 0.6316 (ptt) REVERT: u 16 MET cc_start: 0.5196 (mtt) cc_final: 0.4838 (mmp) REVERT: v 172 LYS cc_start: 0.4618 (tppt) cc_final: 0.4112 (tppt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2355 time to fit residues: 52.7912 Evaluate side-chains 124 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 851 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** u 153 HIS ** 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: 0.4786 moved from start: 0.8913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9909 Z= 0.299 Angle : 0.802 10.505 13410 Z= 0.415 Chirality : 0.044 0.217 1479 Planarity : 0.006 0.065 1735 Dihedral : 5.023 21.014 1346 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % 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: -1.01 (0.23), residues: 1226 helix: 0.54 (0.19), residues: 732 sheet: -1.02 (0.55), residues: 83 loop : -2.84 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP t 152 HIS 0.015 0.002 HIS u 153 PHE 0.028 0.003 PHE v 114 TYR 0.032 0.003 TYR u 33 ARG 0.012 0.001 ARG t 586 ********************** 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 : 1.200 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: t 22 ASP cc_start: 0.4851 (m-30) cc_final: 0.4646 (m-30) REVERT: t 101 MET cc_start: 0.7039 (ptp) cc_final: 0.6771 (ptp) REVERT: t 108 LYS cc_start: 0.8814 (mppt) cc_final: 0.8528 (mtmt) REVERT: t 206 MET cc_start: 0.8943 (mtm) cc_final: 0.8307 (mtp) REVERT: t 209 ASN cc_start: 0.7053 (m110) cc_final: 0.6763 (m110) REVERT: t 314 ILE cc_start: 0.8386 (mt) cc_final: 0.7850 (mt) REVERT: t 428 LEU cc_start: 0.8390 (mp) cc_final: 0.8183 (mp) REVERT: t 511 TYR cc_start: 0.2614 (t80) cc_final: 0.2350 (t80) REVERT: t 580 MET cc_start: 0.2207 (tpp) cc_final: 0.1699 (tpp) REVERT: t 705 MET cc_start: 0.7386 (ptt) cc_final: 0.6673 (ptt) REVERT: u 121 MET cc_start: 0.0451 (tpt) cc_final: -0.0208 (tpt) REVERT: u 162 LEU cc_start: 0.6684 (mt) cc_final: 0.6409 (mt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2500 time to fit residues: 55.1926 Evaluate side-chains 122 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 50.0000 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- 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 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 851 GLN ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** 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 = 0.5048 r_free = 0.5048 target = 0.211968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.196806 restraints weight = 53886.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.198451 restraints weight = 38022.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.199666 restraints weight = 27816.648| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4678 r_free = 0.4678 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4677 r_free = 0.4677 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.8994 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= 0.215 Angle : 0.697 9.427 13410 Z= 0.357 Chirality : 0.042 0.194 1479 Planarity : 0.004 0.040 1735 Dihedral : 4.755 20.847 1346 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.47 % 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: -0.69 (0.24), residues: 1226 helix: 0.79 (0.19), residues: 733 sheet: -0.84 (0.56), residues: 81 loop : -2.73 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 152 HIS 0.007 0.001 HIS u 206 PHE 0.023 0.002 PHE u 45 TYR 0.020 0.002 TYR t 550 ARG 0.006 0.001 ARG t 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.36 seconds wall clock time: 39 minutes 33.64 seconds (2373.64 seconds total)