Starting phenix.real_space_refine on Tue Jun 25 11:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rev_19109/06_2024/8rev_19109_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.022 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 28 5.49 5 S 52 5.16 5 C 4859 2.51 5 N 1360 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 228": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7797 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5735 Classifications: {'peptide': 709} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 681} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1481 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 179} Chain: "E" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 927 SG CYS A 115 83.138 55.612 54.379 1.00108.05 S ATOM 1229 SG CYS A 154 87.610 54.486 58.797 1.00106.73 S ATOM 1065 SG CYS A 133 88.492 51.710 53.382 1.00 96.36 S ATOM 1522 SG CYS A 189 83.804 50.360 57.390 1.00 96.00 S Time building chain proxies: 5.63, per 1000 atoms: 0.72 Number of scatterers: 7797 At special positions: 0 Unit cell: (124.32, 85.68, 78.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 28 15.00 O 1494 8.00 N 1360 7.00 C 4859 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 801 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 154 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 115 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 189 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 133 " Number of angles added : 12 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 5 sheets defined 49.6% alpha, 10.0% beta 4 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 76 through 97 Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 156 through 162 removed outlier: 4.011A pdb=" N ASP A 161 " --> pdb=" O HIS A 157 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.711A pdb=" N ARG A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.903A pdb=" N ASP A 239 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 321 through 343 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 368 through 383 removed outlier: 4.019A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 440 through 449 Proline residue: A 445 - end of helix removed outlier: 3.802A pdb=" N LYS A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 513 through 529 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 630 through 643 Processing helix chain 'A' and resid 647 through 665 removed outlier: 4.285A pdb=" N ARG A 665 " --> pdb=" O GLN A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 684 removed outlier: 3.634A pdb=" N GLN A 684 " --> pdb=" O ARG A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 681 through 684' Processing helix chain 'A' and resid 692 through 697 removed outlier: 4.198A pdb=" N ALA A 697 " --> pdb=" O TRP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'D' and resid 123 through 141 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 273 through 284 removed outlier: 4.259A pdb=" N ALA D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 453 through 456 removed outlier: 7.064A pdb=" N VAL A 230 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A 456 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE A 232 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 106 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 205 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 108 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER A 207 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY A 172 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY A 107 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP A 174 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 251 Processing sheet with id= D, first strand: chain 'A' and resid 492 through 494 removed outlier: 8.013A pdb=" N GLY A 533 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 617 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 535 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N CYS A 619 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 537 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 593 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A 536 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 595 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 538 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS A 597 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 146 through 152 removed outlier: 3.910A pdb=" N LEU D 104 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 210 " --> pdb=" O HIS D 103 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG D 239 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE D 213 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR D 241 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR D 215 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL D 243 " --> pdb=" O TYR D 215 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 3322 1.42 - 1.65: 4604 1.65 - 1.88: 76 1.88 - 2.11: 0 2.11 - 2.34: 12 Bond restraints: 8014 Sorted by residual: bond pdb=" C1' L5R B 83 " pdb=" C2' L5R B 83 " ideal model delta sigma weight residual 1.285 1.518 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1' L5R B 83 " pdb=" O4' L5R B 83 " ideal model delta sigma weight residual 1.609 1.426 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C4' L5R B 83 " pdb=" O4' L5R B 83 " ideal model delta sigma weight residual 1.281 1.440 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C2 L5R B 83 " pdb=" N1 L5R B 83 " ideal model delta sigma weight residual 1.489 1.360 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" S2 SF4 A 801 " pdb="FE3 SF4 A 801 " ideal model delta sigma weight residual 2.280 2.129 0.151 3.00e-02 1.11e+03 2.53e+01 ... (remaining 8009 not shown) Histogram of bond angle deviations from ideal: 67.13 - 89.18: 14 89.18 - 111.23: 3456 111.23 - 133.28: 7480 133.28 - 155.33: 10 155.33 - 177.38: 2 Bond angle restraints: 10962 Sorted by residual: angle pdb=" C26 L5R B 83 " pdb=" C21 L5R B 83 " pdb=" C8 L5R B 83 " ideal model delta sigma weight residual 88.70 120.65 -31.95 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C3' DA E 3 " pdb=" O3' DA E 3 " pdb=" P DA E 4 " ideal model delta sigma weight residual 120.20 107.10 13.10 1.50e+00 4.44e-01 7.63e+01 angle pdb=" C3' DG E 2 " pdb=" O3' DG E 2 " pdb=" P DA E 3 " ideal model delta sigma weight residual 120.20 107.44 12.76 1.50e+00 4.44e-01 7.24e+01 angle pdb=" C3' DT E 5 " pdb=" O3' DT E 5 " pdb=" P DT E 6 " ideal model delta sigma weight residual 120.20 108.74 11.46 1.50e+00 4.44e-01 5.83e+01 angle pdb=" C3' DC E 1 " pdb=" O3' DC E 1 " pdb=" P DG E 2 " ideal model delta sigma weight residual 120.20 109.89 10.31 1.50e+00 4.44e-01 4.72e+01 ... (remaining 10957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 4344 31.63 - 63.26: 394 63.26 - 94.89: 41 94.89 - 126.52: 0 126.52 - 158.15: 4 Dihedral angle restraints: 4783 sinusoidal: 2141 harmonic: 2642 Sorted by residual: dihedral pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " pdb=" NH1 ARG A 256 " ideal model delta sinusoidal sigma weight residual 0.00 87.93 -87.93 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CD ARG A 260 " pdb=" NE ARG A 260 " pdb=" CZ ARG A 260 " pdb=" NH1 ARG A 260 " ideal model delta sinusoidal sigma weight residual 0.00 87.81 -87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CD ARG D 123 " pdb=" NE ARG D 123 " pdb=" CZ ARG D 123 " pdb=" NH1 ARG D 123 " ideal model delta sinusoidal sigma weight residual 0.00 -87.69 87.69 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 4780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1161 0.127 - 0.254: 52 0.254 - 0.381: 6 0.381 - 0.508: 9 0.508 - 0.635: 3 Chirality restraints: 1231 Sorted by residual: chirality pdb=" P DC E 1 " pdb=" OP1 DC E 1 " pdb=" OP2 DC E 1 " pdb=" O5' DC E 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA B 79 " pdb=" OP1 DA B 79 " pdb=" OP2 DA B 79 " pdb=" O5' DA B 79 " both_signs ideal model delta sigma weight residual True 2.35 2.95 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb="FE3 SF4 A 801 " pdb=" S1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False -10.55 -10.01 -0.55 2.00e-01 2.50e+01 7.49e+00 ... (remaining 1228 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' L5R B 83 " 0.813 2.00e-02 2.50e+03 4.18e-01 3.92e+03 pdb=" C2 L5R B 83 " -0.137 2.00e-02 2.50e+03 pdb=" C4 L5R B 83 " 0.085 2.00e-02 2.50e+03 pdb=" C5 L5R B 83 " -0.335 2.00e-02 2.50e+03 pdb=" C6 L5R B 83 " -0.599 2.00e-02 2.50e+03 pdb=" N1 L5R B 83 " 0.033 2.00e-02 2.50e+03 pdb=" N3 L5R B 83 " -0.077 2.00e-02 2.50e+03 pdb=" O2 L5R B 83 " -0.328 2.00e-02 2.50e+03 pdb=" O4 L5R B 83 " 0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 123 " -1.105 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG D 123 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 123 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 123 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 123 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 256 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 256 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 256 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 256 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 256 " 0.015 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 113 2.63 - 3.20: 7406 3.20 - 3.77: 13695 3.77 - 4.33: 18416 4.33 - 4.90: 28975 Nonbonded interactions: 68605 Sorted by model distance: nonbonded pdb=" NH2 ARG A 111 " pdb=" OP2 DA E 11 " model vdw 2.065 2.520 nonbonded pdb=" OD2 ASP A 27 " pdb=" OH TYR A 480 " model vdw 2.206 2.440 nonbonded pdb=" O LEU D 281 " pdb=" OG1 THR D 284 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 338 " pdb=" NH2 ARG A 342 " model vdw 2.216 2.520 nonbonded pdb=" O ASN A 648 " pdb=" OG SER A 652 " model vdw 2.219 2.440 ... (remaining 68600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.460 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: 12.030 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 29.940 Find NCS groups from input model: 0.180 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.008 0.233 8014 Z= 0.474 Angle : 1.090 31.953 10962 Z= 0.632 Chirality : 0.078 0.635 1231 Planarity : 0.039 0.495 1309 Dihedral : 22.250 158.147 3073 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.05 % Favored : 93.72 % Rotamer: Outliers : 5.70 % Allowed : 21.04 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.33 (0.27), residues: 892 helix: 0.12 (0.23), residues: 458 sheet: -2.19 (0.48), residues: 114 loop : -1.73 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 736 HIS 0.007 0.001 HIS A 744 PHE 0.030 0.002 PHE A 717 TYR 0.023 0.002 TYR A 206 ARG 0.007 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6742 (mm) REVERT: D 103 HIS cc_start: 0.5254 (m-70) cc_final: 0.4999 (m90) REVERT: D 109 ASP cc_start: 0.8335 (t0) cc_final: 0.8003 (t0) REVERT: D 172 GLU cc_start: 0.7899 (pp20) cc_final: 0.7423 (pp20) REVERT: D 173 ARG cc_start: 0.8120 (mmp-170) cc_final: 0.7651 (mmp-170) REVERT: D 180 HIS cc_start: 0.7045 (m90) cc_final: 0.6695 (m90) outliers start: 45 outliers final: 10 residues processed: 167 average time/residue: 0.2726 time to fit residues: 57.1196 Evaluate side-chains 114 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain D residue 202 HIS Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 389 ASN A 397 GLN A 511 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8014 Z= 0.285 Angle : 0.715 13.932 10962 Z= 0.349 Chirality : 0.045 0.181 1231 Planarity : 0.006 0.063 1309 Dihedral : 18.906 153.951 1319 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.45 % Allowed : 20.41 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.75 (0.27), residues: 892 helix: 0.75 (0.23), residues: 458 sheet: -1.77 (0.51), residues: 101 loop : -1.83 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 373 HIS 0.007 0.001 HIS A 611 PHE 0.025 0.002 PHE A 717 TYR 0.025 0.002 TYR A 206 ARG 0.006 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 115 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8712 (t) cc_final: 0.8510 (m) REVERT: A 122 ARG cc_start: 0.7640 (mmp80) cc_final: 0.7102 (mmt180) REVERT: A 134 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7265 (tmm-80) REVERT: A 256 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8571 (ptp90) REVERT: A 272 MET cc_start: 0.6983 (mmt) cc_final: 0.6019 (ttt) REVERT: A 378 LEU cc_start: 0.7702 (tp) cc_final: 0.7468 (tt) REVERT: A 656 MET cc_start: 0.8432 (mmm) cc_final: 0.8021 (mmm) REVERT: A 717 PHE cc_start: 0.7919 (t80) cc_final: 0.7715 (t80) REVERT: D 103 HIS cc_start: 0.5629 (m-70) cc_final: 0.5239 (m90) REVERT: D 169 ASP cc_start: 0.8330 (t0) cc_final: 0.8001 (t0) REVERT: D 172 GLU cc_start: 0.7987 (pp20) cc_final: 0.7700 (pp20) REVERT: D 197 ARG cc_start: 0.8844 (tpt-90) cc_final: 0.7797 (tpt-90) outliers start: 43 outliers final: 19 residues processed: 150 average time/residue: 0.1919 time to fit residues: 39.4954 Evaluate side-chains 123 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 64 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8014 Z= 0.243 Angle : 0.660 13.700 10962 Z= 0.318 Chirality : 0.043 0.175 1231 Planarity : 0.004 0.044 1309 Dihedral : 18.498 151.706 1306 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.56 % Allowed : 22.31 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.28), residues: 892 helix: 1.24 (0.23), residues: 448 sheet: -1.61 (0.52), residues: 101 loop : -1.74 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 373 HIS 0.003 0.001 HIS A 433 PHE 0.023 0.002 PHE D 134 TYR 0.023 0.002 TYR A 206 ARG 0.005 0.001 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7635 (mmp80) cc_final: 0.7095 (mmt180) REVERT: A 134 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7220 (tmm-80) REVERT: A 256 ARG cc_start: 0.8674 (tmm-80) cc_final: 0.8360 (ptp90) REVERT: A 263 GLN cc_start: 0.8078 (mm110) cc_final: 0.7865 (mm-40) REVERT: A 272 MET cc_start: 0.7066 (mmt) cc_final: 0.6083 (ttt) REVERT: A 656 MET cc_start: 0.8427 (mmm) cc_final: 0.8067 (mmm) REVERT: A 717 PHE cc_start: 0.8087 (t80) cc_final: 0.7681 (t80) REVERT: D 103 HIS cc_start: 0.5655 (m-70) cc_final: 0.5226 (m90) REVERT: D 169 ASP cc_start: 0.8441 (t0) cc_final: 0.8134 (t0) REVERT: D 172 GLU cc_start: 0.8054 (pp20) cc_final: 0.7798 (pp20) REVERT: D 197 ARG cc_start: 0.8874 (tpt-90) cc_final: 0.7874 (tpt-90) REVERT: D 209 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7066 (mtt-85) outliers start: 36 outliers final: 13 residues processed: 150 average time/residue: 0.1900 time to fit residues: 39.0569 Evaluate side-chains 118 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8014 Z= 0.220 Angle : 0.647 13.293 10962 Z= 0.312 Chirality : 0.044 0.327 1231 Planarity : 0.004 0.042 1309 Dihedral : 18.146 148.029 1300 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.56 % Allowed : 21.67 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 892 helix: 1.44 (0.24), residues: 441 sheet: -1.56 (0.52), residues: 101 loop : -1.65 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 373 HIS 0.004 0.001 HIS D 227 PHE 0.011 0.001 PHE A 717 TYR 0.031 0.002 TYR D 130 ARG 0.005 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 113 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7613 (mmp80) cc_final: 0.7123 (mmt180) REVERT: A 134 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7279 (tmm-80) REVERT: A 256 ARG cc_start: 0.8725 (tmm-80) cc_final: 0.8433 (ptp90) REVERT: A 272 MET cc_start: 0.7073 (mmt) cc_final: 0.6176 (ttt) REVERT: A 656 MET cc_start: 0.8405 (mmm) cc_final: 0.8135 (mmm) REVERT: D 103 HIS cc_start: 0.5569 (m-70) cc_final: 0.5079 (m90) REVERT: D 169 ASP cc_start: 0.8526 (t0) cc_final: 0.8183 (t0) REVERT: D 172 GLU cc_start: 0.8083 (pp20) cc_final: 0.7822 (pp20) REVERT: D 197 ARG cc_start: 0.8878 (tpt-90) cc_final: 0.7908 (tpt-90) REVERT: D 209 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7387 (mtm-85) outliers start: 36 outliers final: 18 residues processed: 145 average time/residue: 0.2035 time to fit residues: 40.2223 Evaluate side-chains 122 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8014 Z= 0.290 Angle : 0.671 12.770 10962 Z= 0.323 Chirality : 0.044 0.175 1231 Planarity : 0.004 0.042 1309 Dihedral : 18.001 147.076 1300 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.45 % Allowed : 22.31 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.28), residues: 892 helix: 1.32 (0.24), residues: 443 sheet: -1.66 (0.50), residues: 101 loop : -1.70 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 373 HIS 0.004 0.001 HIS A 658 PHE 0.029 0.002 PHE D 134 TYR 0.034 0.002 TYR D 130 ARG 0.006 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8067 (pp20) REVERT: A 122 ARG cc_start: 0.7626 (mmp80) cc_final: 0.7108 (mmt180) REVERT: A 134 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7407 (tmm-80) REVERT: A 256 ARG cc_start: 0.8733 (tmm-80) cc_final: 0.8467 (ptp90) REVERT: A 272 MET cc_start: 0.7147 (mmt) cc_final: 0.6290 (ttt) REVERT: A 656 MET cc_start: 0.8425 (mmm) cc_final: 0.8137 (mmm) REVERT: D 103 HIS cc_start: 0.5620 (m-70) cc_final: 0.5098 (m90) REVERT: D 169 ASP cc_start: 0.8616 (t0) cc_final: 0.8391 (t0) REVERT: D 172 GLU cc_start: 0.8059 (pp20) cc_final: 0.7778 (pp20) outliers start: 43 outliers final: 24 residues processed: 147 average time/residue: 0.1895 time to fit residues: 38.1417 Evaluate side-chains 131 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8014 Z= 0.255 Angle : 0.653 13.035 10962 Z= 0.313 Chirality : 0.043 0.170 1231 Planarity : 0.004 0.042 1309 Dihedral : 17.863 146.713 1300 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.06 % Allowed : 23.57 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.28), residues: 892 helix: 1.38 (0.24), residues: 441 sheet: -1.57 (0.51), residues: 100 loop : -1.65 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 373 HIS 0.003 0.001 HIS A 433 PHE 0.028 0.002 PHE D 134 TYR 0.022 0.002 TYR A 206 ARG 0.006 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: A 122 ARG cc_start: 0.7603 (mmp80) cc_final: 0.7116 (mmt180) REVERT: A 134 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7962 (tpp-160) REVERT: A 256 ARG cc_start: 0.8708 (tmm-80) cc_final: 0.8434 (ptp90) REVERT: A 272 MET cc_start: 0.7172 (mmt) cc_final: 0.6251 (ttt) REVERT: A 372 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7791 (mtp180) REVERT: A 656 MET cc_start: 0.8405 (mmm) cc_final: 0.8160 (mmm) REVERT: D 138 TYR cc_start: 0.7204 (t80) cc_final: 0.6404 (t80) REVERT: D 169 ASP cc_start: 0.8647 (t0) cc_final: 0.8429 (t0) REVERT: D 172 GLU cc_start: 0.8086 (pp20) cc_final: 0.7809 (pp20) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.2188 time to fit residues: 40.8209 Evaluate side-chains 128 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8014 Z= 0.240 Angle : 0.655 12.752 10962 Z= 0.312 Chirality : 0.043 0.189 1231 Planarity : 0.004 0.041 1309 Dihedral : 17.746 147.269 1298 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.68 % Allowed : 24.46 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.20 (0.28), residues: 892 helix: 1.37 (0.24), residues: 441 sheet: -1.61 (0.50), residues: 100 loop : -1.64 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 373 HIS 0.003 0.001 HIS A 744 PHE 0.030 0.002 PHE D 134 TYR 0.022 0.001 TYR A 206 ARG 0.005 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7587 (mmp80) cc_final: 0.7116 (mmt180) REVERT: A 134 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7540 (tmm-80) REVERT: A 256 ARG cc_start: 0.8711 (tmm-80) cc_final: 0.8430 (ptp90) REVERT: A 272 MET cc_start: 0.7211 (mmt) cc_final: 0.6247 (ttt) REVERT: A 372 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7768 (mtp180) REVERT: A 484 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6110 (pp) REVERT: A 656 MET cc_start: 0.8409 (mmm) cc_final: 0.8201 (mmm) REVERT: D 138 TYR cc_start: 0.7187 (t80) cc_final: 0.6426 (t80) REVERT: D 209 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7456 (mtm-85) outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 0.1836 time to fit residues: 34.4336 Evaluate side-chains 123 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8014 Z= 0.198 Angle : 0.657 12.969 10962 Z= 0.310 Chirality : 0.042 0.183 1231 Planarity : 0.004 0.041 1309 Dihedral : 17.632 147.955 1297 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 3.68 % Allowed : 25.48 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 892 helix: 1.46 (0.25), residues: 440 sheet: -1.50 (0.51), residues: 100 loop : -1.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 373 HIS 0.003 0.001 HIS A 744 PHE 0.030 0.001 PHE D 134 TYR 0.029 0.001 TYR D 130 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7514 (mmp80) cc_final: 0.7098 (mmt180) REVERT: A 134 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7977 (tpp-160) REVERT: A 256 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8441 (ptp90) REVERT: A 272 MET cc_start: 0.7223 (mmt) cc_final: 0.6245 (ttt) REVERT: A 372 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7767 (mtp180) REVERT: A 717 PHE cc_start: 0.7980 (t80) cc_final: 0.7591 (t80) REVERT: D 138 TYR cc_start: 0.7118 (t80) cc_final: 0.6389 (t80) REVERT: D 209 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: D 285 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7971 (mm) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.1833 time to fit residues: 33.1938 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8014 Z= 0.230 Angle : 0.667 12.683 10962 Z= 0.319 Chirality : 0.043 0.184 1231 Planarity : 0.004 0.040 1309 Dihedral : 17.566 148.817 1297 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 25.98 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.29), residues: 892 helix: 1.41 (0.25), residues: 442 sheet: -1.53 (0.49), residues: 105 loop : -1.62 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 373 HIS 0.004 0.001 HIS A 744 PHE 0.031 0.002 PHE D 134 TYR 0.054 0.002 TYR D 130 ARG 0.004 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.7701 (p) cc_final: 0.7404 (t) REVERT: A 122 ARG cc_start: 0.7527 (mmp80) cc_final: 0.7110 (mmt180) REVERT: A 134 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7950 (tpp-160) REVERT: A 256 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8423 (ptp90) REVERT: A 272 MET cc_start: 0.7219 (mmt) cc_final: 0.6321 (ttt) REVERT: A 372 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7866 (mtp-110) REVERT: A 583 TYR cc_start: 0.6980 (t80) cc_final: 0.6764 (t80) REVERT: D 138 TYR cc_start: 0.7178 (t80) cc_final: 0.6444 (t80) REVERT: D 209 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7591 (mtm-85) REVERT: D 285 ILE cc_start: 0.8275 (mp) cc_final: 0.7935 (mm) outliers start: 25 outliers final: 21 residues processed: 131 average time/residue: 0.1876 time to fit residues: 34.0865 Evaluate side-chains 134 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 56 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8014 Z= 0.218 Angle : 0.683 12.833 10962 Z= 0.322 Chirality : 0.043 0.185 1231 Planarity : 0.004 0.050 1309 Dihedral : 17.499 149.515 1297 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 3.17 % Allowed : 26.49 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.10 (0.29), residues: 892 helix: 1.43 (0.25), residues: 441 sheet: -1.62 (0.49), residues: 109 loop : -1.54 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 373 HIS 0.004 0.001 HIS A 744 PHE 0.032 0.002 PHE D 134 TYR 0.049 0.002 TYR D 130 ARG 0.004 0.000 ARG D 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.7677 (p) cc_final: 0.7360 (t) REVERT: A 122 ARG cc_start: 0.7525 (mmp80) cc_final: 0.7106 (mmt180) REVERT: A 134 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7977 (tpp-160) REVERT: A 256 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8421 (ptp90) REVERT: A 272 MET cc_start: 0.7227 (mmt) cc_final: 0.6298 (ttt) REVERT: A 372 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7932 (mtp-110) REVERT: A 583 TYR cc_start: 0.6981 (t80) cc_final: 0.6737 (t80) REVERT: D 138 TYR cc_start: 0.7168 (t80) cc_final: 0.6423 (t80) REVERT: D 209 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7626 (mtm-85) REVERT: D 285 ILE cc_start: 0.8261 (mp) cc_final: 0.7955 (mm) outliers start: 25 outliers final: 23 residues processed: 126 average time/residue: 0.1810 time to fit residues: 31.8733 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 202 HIS Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102772 restraints weight = 12002.023| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.80 r_work: 0.3363 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8014 Z= 0.288 Angle : 0.703 12.523 10962 Z= 0.335 Chirality : 0.044 0.185 1231 Planarity : 0.004 0.039 1309 Dihedral : 17.483 150.380 1297 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 3.30 % Allowed : 26.36 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.24 (0.29), residues: 892 helix: 1.29 (0.25), residues: 442 sheet: -1.72 (0.47), residues: 114 loop : -1.55 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 373 HIS 0.006 0.001 HIS A 117 PHE 0.033 0.002 PHE D 134 TYR 0.026 0.002 TYR A 206 ARG 0.004 0.001 ARG D 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.22 seconds wall clock time: 38 minutes 15.09 seconds (2295.09 seconds total)