Starting phenix.real_space_refine on Fri Jul 19 10:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/07_2024/8wbx_37426.cif" } resolution = 3.23 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= -0.002 sd= 0.052 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 44 5.16 5 C 4809 2.51 5 N 1202 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.67 Number of scatterers: 7331 At special positions: 0 Unit cell: (80.3, 94.6, 116.6, 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 44 16.00 O 1276 8.00 N 1202 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.572A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.333A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.452A 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 380 through 404 removed outlier: 3.917A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.207A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 472 removed outlier: 3.678A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.810A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 4.509A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.691A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 581 through 594 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.794A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 137 through 141 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 222 removed outlier: 3.671A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 380 through 406 removed outlier: 4.125A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 472 removed outlier: 3.705A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.907A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 4.547A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 4.076A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 512 through 541 Processing helix chain 'B' and resid 543 through 560 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.833A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.638A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.591A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.260A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 264 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 99 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.146A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1371 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: 2.10 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 1304 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7495 Sorted by residual: bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N TYR B 504 " pdb=" CA TYR B 504 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" N PHE A 275 " pdb=" CA PHE A 275 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N GLN B 593 " pdb=" CA GLN B 593 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.64: 142 105.64 - 112.78: 4056 112.78 - 119.92: 2476 119.92 - 127.06: 3409 127.06 - 134.20: 82 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" C PHE B 583 " ideal model delta sigma weight residual 110.97 105.67 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" C PHE B 315 " ideal model delta sigma weight residual 111.36 106.34 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" C ASP B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta sigma weight residual 120.29 114.12 6.17 1.42e+00 4.96e-01 1.89e+01 angle pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O PHE B 583 " pdb=" C PHE B 583 " pdb=" N TYR B 584 " ideal model delta sigma weight residual 122.03 125.37 -3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3966 22.41 - 44.82: 377 44.82 - 67.23: 46 67.23 - 89.64: 3 89.64 - 112.04: 10 Dihedral angle restraints: 4402 sinusoidal: 1720 harmonic: 2682 Sorted by residual: dihedral pdb=" C10 A8S A 701 " pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " ideal model delta sinusoidal sigma weight residual 55.84 -56.20 112.04 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C15 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -49.34 58.90 -108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -169.52 -62.40 -107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 954 0.047 - 0.095: 196 0.095 - 0.142: 43 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA PHE B 583 " pdb=" N PHE B 583 " pdb=" C PHE B 583 " pdb=" CB PHE B 583 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU A 652 " pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CB LEU A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1196 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 582 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR B 582 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 582 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 583 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 233 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2209 2.82 - 3.34: 7366 3.34 - 3.86: 12569 3.86 - 4.38: 13998 4.38 - 4.90: 23990 Nonbonded interactions: 60132 Sorted by model distance: nonbonded pdb=" O THR B 156 " pdb=" OG1 THR B 160 " model vdw 2.305 2.440 nonbonded pdb=" N ASP B 432 " pdb=" OD1 ASP B 432 " model vdw 2.368 2.520 nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 480 " model vdw 2.402 2.440 nonbonded pdb=" O LEU A 528 " pdb=" NH2 ARG A 650 " model vdw 2.410 2.520 nonbonded pdb=" O SER A 444 " pdb=" OH TYR A 526 " model vdw 2.424 2.440 ... (remaining 60127 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' and resid 90 through 660) selection = chain 'B' } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 0.063 7495 Z= 0.186 Angle : 0.658 9.031 10165 Z= 0.351 Chirality : 0.040 0.236 1199 Planarity : 0.004 0.061 1242 Dihedral : 16.957 112.044 2678 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 22.92 % Favored : 76.70 % 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: 1.77 (0.29), residues: 918 helix: 2.00 (0.21), residues: 608 sheet: 0.12 (0.66), residues: 46 loop : -0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 PHE 0.015 0.001 PHE A 499 TYR 0.026 0.001 TYR B 504 ARG 0.008 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.7843 (mt) cc_final: 0.7549 (mp) REVERT: A 506 MET cc_start: 0.6127 (mmp) cc_final: 0.5685 (ttt) REVERT: B 97 MET cc_start: 0.5763 (ttm) cc_final: 0.5535 (ttp) REVERT: B 569 VAL cc_start: 0.7387 (t) cc_final: 0.7135 (t) REVERT: B 575 TRP cc_start: 0.7252 (p-90) cc_final: 0.6630 (t-100) outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.1718 time to fit residues: 39.7172 Evaluate side-chains 150 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7495 Z= 0.207 Angle : 0.592 8.788 10165 Z= 0.280 Chirality : 0.039 0.126 1199 Planarity : 0.004 0.048 1242 Dihedral : 7.634 64.851 1035 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.41 % Allowed : 21.03 % Favored : 74.56 % 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: 1.84 (0.28), residues: 918 helix: 2.00 (0.20), residues: 616 sheet: -0.11 (0.67), residues: 48 loop : -0.40 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.022 0.002 PHE A 275 TYR 0.011 0.001 TYR A 475 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.805 Fit side-chains REVERT: A 310 MET cc_start: 0.8242 (ppp) cc_final: 0.7860 (ppp) REVERT: A 390 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6750 (tt) REVERT: A 555 MET cc_start: 0.6595 (tpt) cc_final: 0.6364 (tpt) REVERT: A 652 LEU cc_start: 0.8288 (mm) cc_final: 0.7840 (tp) REVERT: B 161 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7146 (mm) REVERT: B 390 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6691 (tt) REVERT: B 432 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7169 (p0) REVERT: B 508 TYR cc_start: 0.5938 (t80) cc_final: 0.5712 (t80) REVERT: B 575 TRP cc_start: 0.7461 (p-90) cc_final: 0.6572 (t-100) REVERT: B 652 LEU cc_start: 0.8407 (mm) cc_final: 0.8103 (tp) outliers start: 35 outliers final: 22 residues processed: 183 average time/residue: 0.1709 time to fit residues: 43.0976 Evaluate side-chains 181 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7495 Z= 0.167 Angle : 0.535 8.580 10165 Z= 0.253 Chirality : 0.037 0.116 1199 Planarity : 0.004 0.041 1242 Dihedral : 5.093 50.973 1034 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.53 % Allowed : 23.68 % Favored : 72.80 % 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: 1.84 (0.28), residues: 918 helix: 2.00 (0.20), residues: 616 sheet: -0.35 (0.64), residues: 48 loop : -0.37 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.023 0.001 PHE A 275 TYR 0.010 0.001 TYR B 475 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 0.881 Fit side-chains REVERT: A 310 MET cc_start: 0.8245 (ppp) cc_final: 0.7970 (ppp) REVERT: A 429 ASP cc_start: 0.8013 (m-30) cc_final: 0.7801 (m-30) REVERT: A 432 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7492 (p0) REVERT: A 568 LYS cc_start: 0.7938 (tttt) cc_final: 0.7633 (tttt) REVERT: A 652 LEU cc_start: 0.8360 (mm) cc_final: 0.7880 (tt) REVERT: B 161 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 310 MET cc_start: 0.8413 (ppp) cc_final: 0.8100 (ppp) REVERT: B 432 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7170 (p0) REVERT: B 506 MET cc_start: 0.6614 (mmp) cc_final: 0.6077 (ttt) REVERT: B 508 TYR cc_start: 0.5946 (t80) cc_final: 0.5746 (t80) REVERT: B 568 LYS cc_start: 0.7691 (tttt) cc_final: 0.7444 (tttt) REVERT: B 652 LEU cc_start: 0.8339 (mm) cc_final: 0.7856 (tt) outliers start: 28 outliers final: 16 residues processed: 177 average time/residue: 0.1721 time to fit residues: 41.8823 Evaluate side-chains 171 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7495 Z= 0.188 Angle : 0.544 8.712 10165 Z= 0.255 Chirality : 0.038 0.145 1199 Planarity : 0.004 0.039 1242 Dihedral : 4.513 52.365 1034 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.66 % Allowed : 23.43 % Favored : 71.91 % 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: 1.70 (0.28), residues: 918 helix: 1.93 (0.20), residues: 614 sheet: -0.53 (0.64), residues: 48 loop : -0.47 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.021 0.002 PHE A 275 TYR 0.009 0.001 TYR B 475 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 0.753 Fit side-chains REVERT: A 310 MET cc_start: 0.8304 (ppp) cc_final: 0.7962 (ppp) REVERT: A 482 MET cc_start: 0.7424 (mmt) cc_final: 0.6831 (mmm) REVERT: A 568 LYS cc_start: 0.7970 (tttt) cc_final: 0.7622 (tttt) REVERT: A 652 LEU cc_start: 0.8408 (mm) cc_final: 0.7907 (tt) REVERT: B 161 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7252 (mm) REVERT: B 310 MET cc_start: 0.8437 (ppp) cc_final: 0.7951 (ppp) REVERT: B 390 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6768 (tt) REVERT: B 432 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7313 (p0) REVERT: B 462 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6502 (mt-10) REVERT: B 506 MET cc_start: 0.6593 (mmp) cc_final: 0.5886 (ttt) REVERT: B 568 LYS cc_start: 0.7659 (tttt) cc_final: 0.7402 (tttt) REVERT: B 575 TRP cc_start: 0.7416 (p-90) cc_final: 0.6647 (t-100) outliers start: 37 outliers final: 24 residues processed: 178 average time/residue: 0.1640 time to fit residues: 40.3221 Evaluate side-chains 176 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7495 Z= 0.183 Angle : 0.549 8.651 10165 Z= 0.256 Chirality : 0.038 0.119 1199 Planarity : 0.004 0.036 1242 Dihedral : 4.361 53.678 1034 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.66 % Allowed : 23.30 % Favored : 72.04 % 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: 1.62 (0.28), residues: 918 helix: 1.90 (0.21), residues: 612 sheet: -0.74 (0.62), residues: 48 loop : -0.52 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 575 HIS 0.004 0.001 HIS B 219 PHE 0.019 0.001 PHE A 275 TYR 0.008 0.001 TYR A 475 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.883 Fit side-chains REVERT: A 310 MET cc_start: 0.8334 (ppp) cc_final: 0.8009 (ppp) REVERT: A 432 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7532 (p0) REVERT: A 506 MET cc_start: 0.6161 (mmp) cc_final: 0.5486 (ttt) REVERT: A 568 LYS cc_start: 0.8000 (tttt) cc_final: 0.7653 (tttt) REVERT: A 652 LEU cc_start: 0.8405 (mm) cc_final: 0.7906 (tt) REVERT: B 161 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 273 GLN cc_start: 0.5948 (pp30) cc_final: 0.5215 (mm-40) REVERT: B 310 MET cc_start: 0.8454 (ppp) cc_final: 0.8218 (ppp) REVERT: B 432 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7373 (p0) REVERT: B 462 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6515 (mt-10) REVERT: B 506 MET cc_start: 0.6725 (mmp) cc_final: 0.5970 (ttt) REVERT: B 652 LEU cc_start: 0.8363 (mm) cc_final: 0.7911 (tp) outliers start: 37 outliers final: 30 residues processed: 180 average time/residue: 0.1706 time to fit residues: 42.3234 Evaluate side-chains 187 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7495 Z= 0.161 Angle : 0.553 8.456 10165 Z= 0.253 Chirality : 0.037 0.119 1199 Planarity : 0.004 0.035 1242 Dihedral : 4.207 54.945 1034 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.29 % Allowed : 23.17 % Favored : 71.54 % 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: 1.70 (0.28), residues: 918 helix: 1.96 (0.21), residues: 614 sheet: -0.83 (0.61), residues: 48 loop : -0.49 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.016 0.001 PHE A 275 TYR 0.007 0.001 TYR A 475 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 0.804 Fit side-chains REVERT: A 161 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7490 (mm) REVERT: A 246 VAL cc_start: 0.8170 (t) cc_final: 0.7961 (m) REVERT: A 273 GLN cc_start: 0.5801 (pp30) cc_final: 0.5238 (tp40) REVERT: A 310 MET cc_start: 0.8377 (ppp) cc_final: 0.8041 (ppp) REVERT: A 432 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7542 (p0) REVERT: A 568 LYS cc_start: 0.8032 (tttt) cc_final: 0.7646 (tttt) REVERT: A 652 LEU cc_start: 0.8390 (mm) cc_final: 0.7892 (tt) REVERT: B 161 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7190 (mm) REVERT: B 273 GLN cc_start: 0.5883 (pp30) cc_final: 0.5572 (tp40) REVERT: B 310 MET cc_start: 0.8484 (ppp) cc_final: 0.8233 (ppp) REVERT: B 398 LEU cc_start: 0.7462 (mt) cc_final: 0.7148 (mt) REVERT: B 432 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7321 (p0) REVERT: B 462 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6570 (mt-10) REVERT: B 506 MET cc_start: 0.6659 (mmp) cc_final: 0.5916 (ttt) REVERT: B 652 LEU cc_start: 0.8323 (mm) cc_final: 0.7818 (tp) outliers start: 42 outliers final: 30 residues processed: 183 average time/residue: 0.1713 time to fit residues: 42.9707 Evaluate side-chains 189 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7495 Z= 0.296 Angle : 0.636 8.165 10165 Z= 0.303 Chirality : 0.040 0.131 1199 Planarity : 0.004 0.039 1242 Dihedral : 4.398 56.502 1034 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.42 % Allowed : 23.93 % Favored : 70.65 % 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: 1.12 (0.28), residues: 918 helix: 1.57 (0.21), residues: 610 sheet: -1.67 (0.63), residues: 46 loop : -0.67 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 575 HIS 0.005 0.001 HIS A 219 PHE 0.031 0.002 PHE B 275 TYR 0.008 0.001 TYR B 475 ARG 0.005 0.001 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 159 time to evaluate : 0.787 Fit side-chains REVERT: A 161 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7437 (mm) REVERT: A 432 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7512 (p0) REVERT: A 568 LYS cc_start: 0.8040 (tttt) cc_final: 0.7628 (tttt) REVERT: A 635 MET cc_start: 0.6420 (tpp) cc_final: 0.6072 (tpt) REVERT: A 652 LEU cc_start: 0.8385 (mm) cc_final: 0.7866 (tt) REVERT: B 90 MET cc_start: 0.4936 (tmt) cc_final: 0.4611 (tmm) REVERT: B 161 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7540 (mm) REVERT: B 273 GLN cc_start: 0.5980 (pp30) cc_final: 0.5701 (tp40) REVERT: B 310 MET cc_start: 0.8562 (ppp) cc_final: 0.8286 (ppp) REVERT: B 398 LEU cc_start: 0.7424 (mt) cc_final: 0.7102 (mt) REVERT: B 402 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5969 (ttp80) REVERT: B 432 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7295 (p0) REVERT: B 462 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6416 (mt-10) REVERT: B 652 LEU cc_start: 0.8334 (mm) cc_final: 0.7797 (tp) outliers start: 43 outliers final: 32 residues processed: 184 average time/residue: 0.1889 time to fit residues: 46.8241 Evaluate side-chains 188 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7495 Z= 0.205 Angle : 0.593 9.747 10165 Z= 0.277 Chirality : 0.039 0.165 1199 Planarity : 0.004 0.054 1242 Dihedral : 4.301 58.107 1034 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.53 % Allowed : 24.43 % Favored : 71.03 % 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: 1.31 (0.28), residues: 918 helix: 1.70 (0.21), residues: 610 sheet: -1.68 (0.64), residues: 44 loop : -0.57 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.029 0.002 PHE B 275 TYR 0.011 0.001 TYR A 475 ARG 0.006 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 0.808 Fit side-chains REVERT: A 161 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7364 (mm) REVERT: A 273 GLN cc_start: 0.5974 (pp30) cc_final: 0.5531 (tp40) REVERT: A 310 MET cc_start: 0.8487 (ppp) cc_final: 0.8156 (ppp) REVERT: A 432 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 506 MET cc_start: 0.6102 (mmp) cc_final: 0.5509 (ttt) REVERT: A 568 LYS cc_start: 0.8072 (tttt) cc_final: 0.7647 (tttt) REVERT: A 635 MET cc_start: 0.6314 (tpp) cc_final: 0.6086 (tpt) REVERT: A 652 LEU cc_start: 0.8362 (mm) cc_final: 0.7854 (tt) REVERT: B 161 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7360 (mm) REVERT: B 273 GLN cc_start: 0.5905 (pp30) cc_final: 0.5669 (tp40) REVERT: B 310 MET cc_start: 0.8531 (ppp) cc_final: 0.8261 (ppp) REVERT: B 398 LEU cc_start: 0.7380 (mt) cc_final: 0.7073 (mt) REVERT: B 432 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7371 (p0) REVERT: B 506 MET cc_start: 0.6477 (mmp) cc_final: 0.5943 (ttt) REVERT: B 635 MET cc_start: 0.6951 (mmm) cc_final: 0.6652 (tpp) REVERT: B 652 LEU cc_start: 0.8314 (mm) cc_final: 0.7770 (tp) outliers start: 36 outliers final: 29 residues processed: 175 average time/residue: 0.1751 time to fit residues: 41.7502 Evaluate side-chains 180 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7495 Z= 0.198 Angle : 0.607 11.996 10165 Z= 0.280 Chirality : 0.039 0.148 1199 Planarity : 0.004 0.034 1242 Dihedral : 4.278 58.895 1034 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.79 % Allowed : 24.56 % Favored : 70.65 % 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: 1.33 (0.28), residues: 918 helix: 1.66 (0.21), residues: 618 sheet: -1.76 (0.65), residues: 44 loop : -0.46 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.027 0.002 PHE B 275 TYR 0.011 0.001 TYR A 475 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 0.836 Fit side-chains REVERT: A 159 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6608 (tp30) REVERT: A 161 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7405 (mm) REVERT: A 273 GLN cc_start: 0.5972 (pp30) cc_final: 0.5499 (tp40) REVERT: A 310 MET cc_start: 0.8481 (ppp) cc_final: 0.8147 (ppp) REVERT: A 432 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7562 (p0) REVERT: A 482 MET cc_start: 0.7120 (mmt) cc_final: 0.6621 (mmm) REVERT: A 555 MET cc_start: 0.6936 (tpt) cc_final: 0.6635 (tpt) REVERT: A 568 LYS cc_start: 0.8112 (tttt) cc_final: 0.7642 (tttt) REVERT: A 635 MET cc_start: 0.6312 (tpp) cc_final: 0.6100 (tpt) REVERT: A 652 LEU cc_start: 0.8359 (mm) cc_final: 0.7918 (tt) REVERT: B 161 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7319 (mm) REVERT: B 273 GLN cc_start: 0.5900 (pp30) cc_final: 0.5672 (tp40) REVERT: B 310 MET cc_start: 0.8552 (ppp) cc_final: 0.8258 (ppp) REVERT: B 392 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 398 LEU cc_start: 0.7361 (mt) cc_final: 0.7052 (mt) REVERT: B 432 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7440 (p0) REVERT: B 482 MET cc_start: 0.7002 (mmt) cc_final: 0.6481 (mmm) REVERT: B 506 MET cc_start: 0.6642 (mmp) cc_final: 0.6254 (ttt) REVERT: B 575 TRP cc_start: 0.7462 (p-90) cc_final: 0.6431 (t-100) REVERT: B 635 MET cc_start: 0.6932 (mmm) cc_final: 0.6628 (tpp) REVERT: B 652 LEU cc_start: 0.8322 (mm) cc_final: 0.7762 (tp) outliers start: 38 outliers final: 30 residues processed: 174 average time/residue: 0.1827 time to fit residues: 43.2710 Evaluate side-chains 185 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7495 Z= 0.170 Angle : 0.617 15.132 10165 Z= 0.280 Chirality : 0.040 0.368 1199 Planarity : 0.004 0.035 1242 Dihedral : 4.217 59.818 1034 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.28 % Allowed : 26.07 % Favored : 69.65 % 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: 1.38 (0.28), residues: 918 helix: 1.67 (0.21), residues: 620 sheet: -1.75 (0.64), residues: 44 loop : -0.35 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 575 HIS 0.003 0.001 HIS A 219 PHE 0.024 0.001 PHE B 275 TYR 0.009 0.001 TYR A 475 ARG 0.007 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 0.766 Fit side-chains REVERT: A 159 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6600 (tp30) REVERT: A 161 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7418 (mm) REVERT: A 273 GLN cc_start: 0.5959 (pp30) cc_final: 0.5375 (tp40) REVERT: A 310 MET cc_start: 0.8483 (ppp) cc_final: 0.8153 (ppp) REVERT: A 432 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7570 (p0) REVERT: A 506 MET cc_start: 0.5716 (mmp) cc_final: 0.5437 (ttt) REVERT: A 555 MET cc_start: 0.6906 (tpt) cc_final: 0.6646 (tpt) REVERT: A 652 LEU cc_start: 0.8315 (mm) cc_final: 0.7897 (tt) REVERT: B 161 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7262 (mm) REVERT: B 273 GLN cc_start: 0.5823 (pp30) cc_final: 0.5452 (tp40) REVERT: B 280 LEU cc_start: 0.7163 (tp) cc_final: 0.6887 (mt) REVERT: B 310 MET cc_start: 0.8539 (ppp) cc_final: 0.8256 (ppp) REVERT: B 398 LEU cc_start: 0.7340 (mt) cc_final: 0.7030 (mt) REVERT: B 402 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5373 (ptm-80) REVERT: B 432 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7434 (p0) REVERT: B 482 MET cc_start: 0.7062 (mmt) cc_final: 0.6546 (mmm) REVERT: B 506 MET cc_start: 0.6622 (mmp) cc_final: 0.6131 (ttt) REVERT: B 575 TRP cc_start: 0.7467 (p-90) cc_final: 0.6293 (t-100) REVERT: B 635 MET cc_start: 0.6899 (mmm) cc_final: 0.6593 (tpp) REVERT: B 652 LEU cc_start: 0.8322 (mm) cc_final: 0.7781 (tp) outliers start: 34 outliers final: 27 residues processed: 178 average time/residue: 0.1998 time to fit residues: 48.8656 Evaluate side-chains 184 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.172462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146427 restraints weight = 10194.032| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.89 r_work: 0.3986 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7495 Z= 0.218 Angle : 0.642 15.405 10165 Z= 0.293 Chirality : 0.040 0.309 1199 Planarity : 0.004 0.033 1242 Dihedral : 4.264 59.962 1034 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.53 % Allowed : 25.94 % Favored : 69.52 % 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: 1.24 (0.28), residues: 918 helix: 1.56 (0.21), residues: 620 sheet: -1.91 (0.65), residues: 44 loop : -0.37 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.026 0.002 PHE B 275 TYR 0.009 0.001 TYR A 475 ARG 0.007 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.22 seconds wall clock time: 33 minutes 48.24 seconds (2028.24 seconds total)