Starting phenix.real_space_refine on Sat Feb 17 11:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9o_29873/02_2024/8g9o_29873_trim_updated.pdb" } resolution = 4.4 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= 0.002 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 52 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5886 2.51 5 N 1619 2.21 5 O 1872 1.98 5 H 9023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18504 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 13976 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 822} Chain breaks: 2 Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3004 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 856 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 627 Unusual residues: {'DOC': 1, 'GTP': 1} Classifications: {'DNA': 10, 'RNA': 8, 'undetermined': 2} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 17, None: 2} Not linked: pdbres="GTP D 1 " pdbres=" G D 2 " Not linked: pdbres=" DG D 19 " pdbres="DOC D 20 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15568 SG CYS B 373 46.480 23.582 27.128 1.00244.93 S ATOM 15816 SG CYS B 390 40.223 22.178 29.121 1.00250.87 S ATOM 16468 SG CYS B 430 41.979 21.965 22.964 1.00277.19 S ATOM 14227 SG CYS B 293 41.759 27.615 26.238 1.00301.17 S Time building chain proxies: 8.35, per 1000 atoms: 0.45 Number of scatterers: 18504 At special positions: 0 Unit cell: (105.105, 102.375, 152.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 46 16.00 P 52 15.00 Mg 2 11.99 O 1872 8.00 N 1619 7.00 C 5886 6.00 H 9023 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.96 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 293 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 390 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 373 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 430 " Number of angles added : 12 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 43.0% alpha, 12.8% beta 17 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 9.99 Creating SS restraints... Processing helix chain 'A' and resid 410 through 425 removed outlier: 3.784A pdb=" N VAL A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.652A pdb=" N ALA A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 725 through 729 removed outlier: 3.709A pdb=" N ARG A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 725 through 729' Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.614A pdb=" N MET A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 797 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 925 Processing helix chain 'A' and resid 932 through 956 removed outlier: 4.088A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 4.481A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1082 through 1096 Processing helix chain 'A' and resid 1101 through 1121 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1184 through 1187 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1213 through 1219 Processing helix chain 'A' and resid 1228 through 1235 Processing helix chain 'B' and resid 280 through 288 removed outlier: 4.133A pdb=" N GLY B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.787A pdb=" N LYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 removed outlier: 4.160A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 450 through 461 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.709A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 350 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N VAL A 358 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS A 381 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 520 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 389 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 5.765A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 7.130A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1001 through 1005 removed outlier: 6.333A pdb=" N ASP A 859 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE A1036 " --> pdb=" O ASP A 859 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1134 366 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 16.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 9006 1.13 - 1.42: 4039 1.42 - 1.70: 5688 1.70 - 1.99: 63 1.99 - 2.28: 12 Bond restraints: 18808 Sorted by residual: bond pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " ideal model delta sigma weight residual 1.284 1.540 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C4' DOC D 20 " pdb=" C3' DOC D 20 " ideal model delta sigma weight residual 1.334 1.547 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.443 -0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" C4 DGT A1501 " pdb=" N3 DGT A1501 " ideal model delta sigma weight residual 1.502 1.333 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" O4' DOC D 20 " pdb=" C1' DOC D 20 " ideal model delta sigma weight residual 1.268 1.437 -0.169 2.00e-02 2.50e+03 7.11e+01 ... (remaining 18803 not shown) Histogram of bond angle deviations from ideal: 73.47 - 85.64: 12 85.64 - 97.81: 0 97.81 - 109.98: 16128 109.98 - 122.15: 14978 122.15 - 134.32: 2957 Bond angle restraints: 34075 Sorted by residual: angle pdb=" PB GTP D 1 " pdb=" O3B GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 120.50 131.67 -11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" PA GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sigma weight residual 120.50 131.26 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" C4' GTP D 1 " ideal model delta sigma weight residual 111.00 100.27 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" OP1 DOC D 20 " pdb=" P DOC D 20 " pdb=" OP2 DOC D 20 " ideal model delta sigma weight residual 109.57 119.69 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C1' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " ideal model delta sigma weight residual 111.00 101.20 9.80 3.00e+00 1.11e-01 1.07e+01 ... (remaining 34070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 8046 28.96 - 57.92: 582 57.92 - 86.88: 53 86.88 - 115.84: 3 115.84 - 144.80: 4 Dihedral angle restraints: 8688 sinusoidal: 5043 harmonic: 3645 Sorted by residual: dihedral pdb=" O3B GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual -68.92 75.88 -144.80 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" C5' GTP D 1 " pdb=" O5' GTP D 1 " pdb=" PA GTP D 1 " pdb=" O3A GTP D 1 " ideal model delta sinusoidal sigma weight residual 69.27 -64.57 133.83 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O5' GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PA GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sinusoidal sigma weight residual 274.12 144.59 129.53 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 8685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1323 0.066 - 0.131: 163 0.131 - 0.197: 8 0.197 - 0.262: 2 0.262 - 0.328: 2 Chirality restraints: 1498 Sorted by residual: chirality pdb=" C3' DGT A1501 " pdb=" C2' DGT A1501 " pdb=" C4' DGT A1501 " pdb=" O3' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.75 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C2' GTP D 1 " pdb=" C1' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" O2' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C4' GTP D 1 " pdb=" O3' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1495 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1184 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ALA A1184 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A1184 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A1185 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 19 " -0.020 2.00e-02 2.50e+03 7.83e-03 2.14e+00 pdb=" N9 DG D 19 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DG D 19 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG D 19 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG D 19 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG D 19 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 19 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 19 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG D 19 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG D 19 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG D 19 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG D 19 " 0.005 2.00e-02 2.50e+03 pdb=" H8 DG D 19 " -0.003 2.00e-02 2.50e+03 pdb=" H1 DG D 19 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1149 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C PRO A1149 " -0.023 2.00e-02 2.50e+03 pdb=" O PRO A1149 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A1150 " 0.008 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 492 2.13 - 2.75: 33221 2.75 - 3.37: 51470 3.37 - 3.98: 65151 3.98 - 4.60: 101723 Nonbonded interactions: 252057 Sorted by model distance: nonbonded pdb=" H ASN A 549 " pdb=" O GLN A 554 " model vdw 1.518 1.850 nonbonded pdb=" H SER B 278 " pdb=" OE1 GLN B 281 " model vdw 1.601 1.850 nonbonded pdb=" H GLN A1177 " pdb=" O SER A1201 " model vdw 1.606 1.850 nonbonded pdb=" HH TYR B 368 " pdb=" OP2 DT C 37 " model vdw 1.613 1.850 nonbonded pdb=" H THR A1136 " pdb=" OH TYR A1142 " model vdw 1.614 1.850 ... (remaining 252052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.250 Extract box with map and model: 3.890 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 72.150 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.256 9785 Z= 0.470 Angle : 0.582 11.167 13459 Z= 0.306 Chirality : 0.044 0.328 1498 Planarity : 0.003 0.029 1549 Dihedral : 19.862 144.802 3817 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 19.64 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.15 (0.27), residues: 1046 helix: 1.86 (0.24), residues: 476 sheet: 0.62 (0.41), residues: 140 loop : -0.40 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1156 HIS 0.003 0.001 HIS B 438 PHE 0.008 0.001 PHE A 622 TYR 0.008 0.001 TYR B 359 ARG 0.004 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 648 LEU cc_start: 0.9232 (mt) cc_final: 0.8980 (mt) REVERT: A 768 ILE cc_start: 0.9701 (mt) cc_final: 0.9395 (tp) REVERT: B 343 ASP cc_start: 0.8807 (m-30) cc_final: 0.8099 (t0) REVERT: B 396 ASP cc_start: 0.9497 (m-30) cc_final: 0.9268 (p0) REVERT: B 433 TYR cc_start: 0.9517 (t80) cc_final: 0.9257 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.6490 time to fit residues: 117.1151 Evaluate side-chains 85 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS A 799 ASN ** A1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 ASN B 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9785 Z= 0.349 Angle : 0.637 8.172 13459 Z= 0.348 Chirality : 0.042 0.194 1498 Planarity : 0.004 0.043 1549 Dihedral : 17.879 136.189 1693 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.39 (0.26), residues: 1046 helix: 1.08 (0.23), residues: 483 sheet: 0.30 (0.41), residues: 140 loop : -0.66 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1080 HIS 0.009 0.002 HIS B 309 PHE 0.016 0.002 PHE A1015 TYR 0.012 0.002 TYR A 953 ARG 0.010 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 485 GLU cc_start: 0.8408 (tt0) cc_final: 0.8107 (tp30) REVERT: A 952 MET cc_start: 0.8516 (ttt) cc_final: 0.7987 (tmm) REVERT: B 327 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9031 (mm-30) REVERT: B 343 ASP cc_start: 0.9125 (m-30) cc_final: 0.8761 (t0) REVERT: B 396 ASP cc_start: 0.9590 (m-30) cc_final: 0.9311 (p0) REVERT: B 425 HIS cc_start: 0.9362 (m90) cc_final: 0.9016 (m90) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.5631 time to fit residues: 62.3034 Evaluate side-chains 67 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 ASN A 737 HIS ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 991 ASN ** A1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS A1195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9785 Z= 0.436 Angle : 0.727 14.083 13459 Z= 0.400 Chirality : 0.044 0.319 1498 Planarity : 0.005 0.056 1549 Dihedral : 17.945 130.986 1693 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.93 (0.25), residues: 1046 helix: -0.18 (0.22), residues: 477 sheet: -0.11 (0.40), residues: 146 loop : -1.20 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1080 HIS 0.008 0.002 HIS B 425 PHE 0.025 0.003 PHE B 392 TYR 0.015 0.002 TYR A 953 ARG 0.005 0.001 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9012 (tpp) cc_final: 0.8809 (tpp) REVERT: A 485 GLU cc_start: 0.8649 (tt0) cc_final: 0.8248 (tp30) REVERT: A 756 MET cc_start: 0.8997 (tmm) cc_final: 0.8794 (tmm) REVERT: A 781 MET cc_start: 0.9219 (ttm) cc_final: 0.8697 (mtp) REVERT: A 952 MET cc_start: 0.8382 (ttt) cc_final: 0.8056 (tmm) REVERT: B 396 ASP cc_start: 0.9608 (m-30) cc_final: 0.9360 (p0) outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.6351 time to fit residues: 60.7776 Evaluate side-chains 60 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9785 Z= 0.246 Angle : 0.555 7.376 13459 Z= 0.307 Chirality : 0.040 0.167 1498 Planarity : 0.004 0.045 1549 Dihedral : 17.664 123.450 1693 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1046 helix: 0.49 (0.23), residues: 477 sheet: -0.05 (0.40), residues: 142 loop : -0.97 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.005 0.001 HIS A 794 PHE 0.015 0.002 PHE B 392 TYR 0.017 0.001 TYR B 353 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 485 GLU cc_start: 0.8536 (tt0) cc_final: 0.8041 (tp30) REVERT: A 756 MET cc_start: 0.8866 (tmm) cc_final: 0.8643 (tmm) REVERT: A 952 MET cc_start: 0.8330 (ttt) cc_final: 0.7899 (tmm) REVERT: B 396 ASP cc_start: 0.9608 (m-30) cc_final: 0.9382 (p0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.5331 time to fit residues: 49.3013 Evaluate side-chains 60 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS A 737 HIS ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9785 Z= 0.295 Angle : 0.573 7.223 13459 Z= 0.320 Chirality : 0.041 0.145 1498 Planarity : 0.004 0.047 1549 Dihedral : 17.750 127.996 1693 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.38 (0.25), residues: 1046 helix: 0.42 (0.23), residues: 478 sheet: -0.21 (0.40), residues: 144 loop : -0.95 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.007 0.002 HIS B 425 PHE 0.012 0.002 PHE B 392 TYR 0.016 0.001 TYR A 706 ARG 0.004 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9239 (mt) cc_final: 0.9027 (mt) REVERT: A 732 TYR cc_start: 0.6661 (m-80) cc_final: 0.6292 (m-80) REVERT: A 756 MET cc_start: 0.8876 (tmm) cc_final: 0.8661 (tmm) REVERT: A 952 MET cc_start: 0.8298 (ttt) cc_final: 0.7945 (tmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.5251 time to fit residues: 47.2780 Evaluate side-chains 58 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9785 Z= 0.311 Angle : 0.592 7.750 13459 Z= 0.330 Chirality : 0.041 0.139 1498 Planarity : 0.004 0.050 1549 Dihedral : 17.829 127.951 1693 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1046 helix: 0.33 (0.23), residues: 474 sheet: -0.59 (0.39), residues: 144 loop : -0.95 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.008 0.002 HIS B 425 PHE 0.017 0.002 PHE B 392 TYR 0.015 0.002 TYR A 706 ARG 0.004 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 MET cc_start: 0.8912 (tmm) cc_final: 0.8595 (tmm) REVERT: A 952 MET cc_start: 0.8310 (ttt) cc_final: 0.7961 (tmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.5117 time to fit residues: 48.5498 Evaluate side-chains 57 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9785 Z= 0.199 Angle : 0.519 7.910 13459 Z= 0.285 Chirality : 0.040 0.165 1498 Planarity : 0.004 0.041 1549 Dihedral : 17.669 129.638 1693 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.03 (0.26), residues: 1046 helix: 0.84 (0.24), residues: 476 sheet: -0.33 (0.40), residues: 141 loop : -0.70 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 333 HIS 0.006 0.001 HIS B 449 PHE 0.012 0.001 PHE B 392 TYR 0.014 0.001 TYR A 953 ARG 0.003 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.6557 (m-80) cc_final: 0.6339 (m-80) REVERT: A 952 MET cc_start: 0.8272 (ttt) cc_final: 0.7881 (tmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.5779 time to fit residues: 54.9918 Evaluate side-chains 60 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9785 Z= 0.272 Angle : 0.559 7.853 13459 Z= 0.311 Chirality : 0.040 0.135 1498 Planarity : 0.004 0.043 1549 Dihedral : 17.764 139.580 1693 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1046 helix: 0.64 (0.23), residues: 474 sheet: -0.50 (0.40), residues: 141 loop : -0.81 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.006 0.001 HIS B 425 PHE 0.015 0.002 PHE B 392 TYR 0.027 0.002 TYR A 790 ARG 0.004 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.6286 (m-80) cc_final: 0.6076 (m-80) REVERT: A 952 MET cc_start: 0.8292 (ttt) cc_final: 0.7952 (tmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.5478 time to fit residues: 49.6235 Evaluate side-chains 59 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9785 Z= 0.148 Angle : 0.493 8.201 13459 Z= 0.267 Chirality : 0.039 0.136 1498 Planarity : 0.003 0.034 1549 Dihedral : 17.584 145.013 1693 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.27), residues: 1046 helix: 1.22 (0.24), residues: 477 sheet: -0.23 (0.41), residues: 141 loop : -0.51 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 498 HIS 0.005 0.001 HIS B 449 PHE 0.013 0.001 PHE B 285 TYR 0.014 0.001 TYR A 953 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 952 MET cc_start: 0.8246 (ttt) cc_final: 0.7830 (tmm) REVERT: A 986 MET cc_start: 0.8671 (mmp) cc_final: 0.8222 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.5125 time to fit residues: 46.0309 Evaluate side-chains 60 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9785 Z= 0.190 Angle : 0.503 7.936 13459 Z= 0.276 Chirality : 0.039 0.130 1498 Planarity : 0.004 0.035 1549 Dihedral : 17.549 144.157 1693 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.45 (0.27), residues: 1046 helix: 1.25 (0.24), residues: 478 sheet: -0.21 (0.41), residues: 141 loop : -0.53 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 659 HIS 0.005 0.001 HIS B 449 PHE 0.011 0.001 PHE B 392 TYR 0.014 0.001 TYR A 953 ARG 0.003 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 781 MET cc_start: 0.9117 (ttm) cc_final: 0.8353 (mtp) REVERT: A 952 MET cc_start: 0.8256 (ttt) cc_final: 0.7879 (tmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.5136 time to fit residues: 47.8077 Evaluate side-chains 58 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 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 = 0.3022 r_free = 0.3022 target = 0.033517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.024214 restraints weight = 281451.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.025381 restraints weight = 164008.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.026188 restraints weight = 113799.892| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9785 Z= 0.171 Angle : 0.493 8.132 13459 Z= 0.269 Chirality : 0.039 0.130 1498 Planarity : 0.003 0.038 1549 Dihedral : 17.458 147.311 1693 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.60 (0.27), residues: 1046 helix: 1.38 (0.24), residues: 478 sheet: -0.12 (0.41), residues: 141 loop : -0.48 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 659 HIS 0.004 0.001 HIS B 449 PHE 0.017 0.001 PHE B 285 TYR 0.014 0.001 TYR A 953 ARG 0.003 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3952.32 seconds wall clock time: 71 minutes 19.39 seconds (4279.39 seconds total)