Starting phenix.real_space_refine on Fri Dec 8 09:25:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd6_37455/12_2023/8wd6_37455.pdb" } resolution = 2.87 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= -0.004 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5206 2.51 5 N 1325 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7973 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3983 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain breaks: 4 Chain: "B" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3990 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain breaks: 4 Time building chain proxies: 4.63, per 1000 atoms: 0.58 Number of scatterers: 7973 At special positions: 0 Unit cell: (82.125, 101.835, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1390 8.00 N 1325 7.00 C 5206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 68.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.690A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.610A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.918A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 3.538A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.502A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 379 through 406 removed outlier: 5.016A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.532A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.534A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.305A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.824A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.779A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.562A pdb=" N TYR A 578 " --> pdb=" O TRP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.586A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.514A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.568A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.548A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 4.144A pdb=" N ARG B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 220 removed outlier: 4.172A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.506A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.591A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 4.535A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 379 through 406 removed outlier: 5.045A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 455 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.546A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.503A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.780A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.755A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET B 576 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.568A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 604 Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.805A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.657A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.645A pdb=" N GLY A 89 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 42 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 removed outlier: 7.171A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.694A pdb=" N LYS B 126 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.041A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2474 1.34 - 1.46: 1890 1.46 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 8143 Sorted by residual: bond pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 1.00e+01 bond pdb=" N PHE A 459 " pdb=" CA PHE A 459 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.00e+00 bond pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.41e-02 5.03e+03 7.12e+00 bond pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.67e+00 ... (remaining 8138 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 149 106.03 - 113.02: 4469 113.02 - 120.01: 2804 120.01 - 126.99: 3523 126.99 - 133.98: 85 Bond angle restraints: 11030 Sorted by residual: angle pdb=" C PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta sigma weight residual 110.85 117.56 -6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA LYS B 140 " pdb=" CB LYS B 140 " pdb=" CG LYS B 140 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" O PHE A 459 " ideal model delta sigma weight residual 118.73 115.50 3.23 9.80e-01 1.04e+00 1.08e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 120.77 123.90 -3.13 9.70e-01 1.06e+00 1.04e+01 angle pdb=" CA CYS B 622 " pdb=" C CYS B 622 " pdb=" O CYS B 622 " ideal model delta sigma weight residual 120.42 117.22 3.20 1.06e+00 8.90e-01 9.11e+00 ... (remaining 11025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4001 16.25 - 32.49: 565 32.49 - 48.74: 179 48.74 - 64.99: 26 64.99 - 81.23: 9 Dihedral angle restraints: 4780 sinusoidal: 1855 harmonic: 2925 Sorted by residual: dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 622 " pdb=" CB CYS B 622 " ideal model delta sinusoidal sigma weight residual 93.00 135.71 -42.71 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" C PHE A 299 " pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta harmonic sigma weight residual -122.60 -132.61 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 134.54 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1122 0.055 - 0.109: 159 0.109 - 0.164: 21 0.164 - 0.219: 2 0.219 - 0.273: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1303 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 598 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" CD GLU B 598 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU B 598 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 463 " 0.226 9.50e-02 1.11e+02 1.01e-01 6.45e+00 pdb=" NE ARG B 463 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 463 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 463 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 463 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 314 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" CG ASP A 314 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 314 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 314 " -0.013 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3277 2.93 - 3.42: 7771 3.42 - 3.91: 12625 3.91 - 4.41: 13867 4.41 - 4.90: 24153 Nonbonded interactions: 61693 Sorted by model distance: nonbonded pdb=" O LEU A 409 " pdb=" NE2 GLN A 413 " model vdw 2.431 2.520 nonbonded pdb=" O GLU A 183 " pdb=" OE1 GLU A 183 " model vdw 2.436 3.040 nonbonded pdb=" OG SER B 405 " pdb=" OE2 GLU B 492 " model vdw 2.439 2.440 nonbonded pdb=" O ARG A 141 " pdb=" N SER A 226 " model vdw 2.452 2.520 nonbonded pdb=" O GLN A 137 " pdb=" NZ LYS A 140 " model vdw 2.453 2.520 ... (remaining 61688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 35 through 119 or resid 125 through 660)) } 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: 2.200 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: 3.980 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.003 0.049 8143 Z= 0.194 Angle : 0.563 8.682 11030 Z= 0.309 Chirality : 0.040 0.273 1306 Planarity : 0.005 0.101 1351 Dihedral : 16.494 81.232 2896 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.12 % Allowed : 31.10 % Favored : 68.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1005 helix: 1.98 (0.21), residues: 649 sheet: 0.04 (0.72), residues: 70 loop : -0.83 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.004 0.001 HIS B 395 PHE 0.026 0.001 PHE B 36 TYR 0.007 0.001 TYR B 480 ARG 0.007 0.001 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 0.780 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 1.2528 time to fit residues: 192.1994 Evaluate side-chains 125 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1153 time to fit residues: 1.4479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.0318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8143 Z= 0.201 Angle : 0.510 6.853 11030 Z= 0.259 Chirality : 0.039 0.130 1306 Planarity : 0.004 0.033 1351 Dihedral : 3.687 14.796 1105 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.66 % Allowed : 29.02 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.28), residues: 1005 helix: 2.09 (0.21), residues: 654 sheet: -0.20 (0.68), residues: 69 loop : -0.52 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 426 HIS 0.004 0.001 HIS B 219 PHE 0.014 0.002 PHE A 624 TYR 0.008 0.001 TYR B 430 ARG 0.003 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 165 average time/residue: 1.1793 time to fit residues: 206.6724 Evaluate side-chains 148 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 9 average time/residue: 0.6557 time to fit residues: 7.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 265 HIS B 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8143 Z= 0.447 Angle : 0.679 7.884 11030 Z= 0.345 Chirality : 0.046 0.168 1306 Planarity : 0.005 0.033 1351 Dihedral : 4.166 17.574 1105 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.13 % Allowed : 29.60 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1005 helix: 1.42 (0.20), residues: 652 sheet: -0.06 (0.59), residues: 82 loop : -0.94 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 426 HIS 0.007 0.001 HIS B 219 PHE 0.017 0.002 PHE B 275 TYR 0.013 0.003 TYR A 526 ARG 0.007 0.001 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 136 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 173 average time/residue: 1.0374 time to fit residues: 191.7433 Evaluate side-chains 156 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.2873 time to fit residues: 4.0614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8143 Z= 0.195 Angle : 0.527 7.780 11030 Z= 0.266 Chirality : 0.039 0.130 1306 Planarity : 0.003 0.029 1351 Dihedral : 3.829 15.335 1105 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.90 % Allowed : 29.94 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.28), residues: 1005 helix: 1.83 (0.21), residues: 655 sheet: -0.40 (0.62), residues: 78 loop : -0.78 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.002 0.001 HIS B 219 PHE 0.018 0.001 PHE A 624 TYR 0.007 0.001 TYR A 430 ARG 0.003 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 0.864 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 173 average time/residue: 1.0753 time to fit residues: 198.2857 Evaluate side-chains 157 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.5861 time to fit residues: 3.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.0020 chunk 40 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8143 Z= 0.224 Angle : 0.557 8.050 11030 Z= 0.279 Chirality : 0.039 0.133 1306 Planarity : 0.003 0.030 1351 Dihedral : 3.800 15.136 1105 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.20 % Allowed : 30.87 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 1005 helix: 1.84 (0.21), residues: 656 sheet: -0.12 (0.60), residues: 83 loop : -0.94 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS B 219 PHE 0.018 0.001 PHE A 624 TYR 0.008 0.001 TYR A 526 ARG 0.004 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 0.910 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 33 residues processed: 165 average time/residue: 1.0497 time to fit residues: 185.0179 Evaluate side-chains 152 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.1292 time to fit residues: 2.2064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8143 Z= 0.339 Angle : 0.619 8.625 11030 Z= 0.312 Chirality : 0.042 0.148 1306 Planarity : 0.004 0.030 1351 Dihedral : 4.020 16.132 1105 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.66 % Allowed : 30.75 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 1005 helix: 1.61 (0.21), residues: 652 sheet: -0.29 (0.61), residues: 78 loop : -0.89 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 426 HIS 0.004 0.001 HIS B 219 PHE 0.016 0.002 PHE A 624 TYR 0.010 0.002 TYR B 526 ARG 0.007 0.001 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 0.894 Fit side-chains outliers start: 49 outliers final: 32 residues processed: 162 average time/residue: 1.0339 time to fit residues: 179.1836 Evaluate side-chains 152 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.3164 time to fit residues: 3.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8143 Z= 0.182 Angle : 0.545 8.422 11030 Z= 0.271 Chirality : 0.039 0.128 1306 Planarity : 0.003 0.029 1351 Dihedral : 3.776 14.820 1105 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.74 % Allowed : 31.56 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 1005 helix: 1.92 (0.21), residues: 654 sheet: -0.42 (0.60), residues: 83 loop : -0.78 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.002 0.001 HIS B 484 PHE 0.017 0.001 PHE A 624 TYR 0.006 0.001 TYR B 480 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 0.930 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 164 average time/residue: 1.0013 time to fit residues: 176.3442 Evaluate side-chains 153 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 1.7337 time to fit residues: 4.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8143 Z= 0.279 Angle : 0.592 8.695 11030 Z= 0.297 Chirality : 0.041 0.139 1306 Planarity : 0.004 0.030 1351 Dihedral : 3.914 15.203 1105 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.32 % Allowed : 30.98 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 1005 helix: 1.75 (0.21), residues: 655 sheet: -0.22 (0.62), residues: 78 loop : -0.98 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 426 HIS 0.004 0.001 HIS B 219 PHE 0.016 0.002 PHE A 624 TYR 0.009 0.002 TYR B 526 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 0.881 Fit side-chains outliers start: 46 outliers final: 33 residues processed: 160 average time/residue: 1.0186 time to fit residues: 174.6366 Evaluate side-chains 158 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.5129 time to fit residues: 4.1214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8143 Z= 0.221 Angle : 0.575 8.808 11030 Z= 0.288 Chirality : 0.039 0.128 1306 Planarity : 0.003 0.035 1351 Dihedral : 3.845 14.768 1105 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.16 % Allowed : 32.49 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 1005 helix: 1.86 (0.21), residues: 653 sheet: -0.54 (0.60), residues: 83 loop : -0.84 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.003 0.001 HIS B 219 PHE 0.016 0.001 PHE A 624 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 0.805 Fit side-chains outliers start: 36 outliers final: 35 residues processed: 154 average time/residue: 1.1211 time to fit residues: 184.0648 Evaluate side-chains 157 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 6 average time/residue: 0.8754 time to fit residues: 6.9784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8143 Z= 0.224 Angle : 0.583 8.759 11030 Z= 0.288 Chirality : 0.039 0.129 1306 Planarity : 0.003 0.032 1351 Dihedral : 3.853 15.593 1105 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.58 % Allowed : 32.95 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 1005 helix: 1.89 (0.21), residues: 649 sheet: -0.65 (0.59), residues: 83 loop : -0.83 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS B 219 PHE 0.017 0.002 PHE B 304 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG B 658 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.930 Fit side-chains outliers start: 31 outliers final: 28 residues processed: 149 average time/residue: 1.1529 time to fit residues: 183.6458 Evaluate side-chains 150 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 1.2285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 4 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120877 restraints weight = 9655.978| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.09 r_work: 0.3273 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8143 Z= 0.221 Angle : 0.578 8.737 11030 Z= 0.289 Chirality : 0.039 0.128 1306 Planarity : 0.003 0.030 1351 Dihedral : 3.839 16.655 1105 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.70 % Allowed : 33.18 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.28), residues: 1005 helix: 1.91 (0.21), residues: 648 sheet: -0.72 (0.59), residues: 84 loop : -0.76 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS B 219 PHE 0.015 0.001 PHE A 624 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG B 658 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.46 seconds wall clock time: 60 minutes 48.54 seconds (3648.54 seconds total)