Starting phenix.real_space_refine on Wed Feb 14 06:51:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5d_31723/02_2024/7v5d_31723_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 40 5.16 5 C 5652 2.51 5 N 1491 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4392 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4379 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.58 Number of scatterers: 8822 At special positions: 0 Unit cell: (80.51, 108.73, 137.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 1 15.00 O 1638 8.00 N 1491 7.00 C 5652 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: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 61.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 178 through 213 removed outlier: 3.841A pdb=" N VAL A 181 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA A 182 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 201 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 230 through 263 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.840A pdb=" N GLU A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 320 removed outlier: 4.510A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 377 Proline residue: A 333 - end of helix removed outlier: 3.991A pdb=" N THR A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 432 removed outlier: 4.505A pdb=" N VAL A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 471 removed outlier: 5.014A pdb=" N SER A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.688A pdb=" N GLU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 641 through 653 removed outlier: 4.017A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 733 through 736 No H-bonds generated for 'chain 'A' and resid 733 through 736' Processing helix chain 'B' and resid 170 through 173 No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 178 through 213 removed outlier: 3.982A pdb=" N VAL B 181 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 201 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Proline residue: B 202 - end of helix removed outlier: 3.504A pdb=" N VAL B 213 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 230 through 263 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 280 through 297 removed outlier: 4.471A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 320 Processing helix chain 'B' and resid 322 through 369 Proline residue: B 333 - end of helix removed outlier: 4.314A pdb=" N THR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 381 through 433 removed outlier: 4.336A pdb=" N VAL B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 473 removed outlier: 3.933A pdb=" N TYR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 592 through 595 No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 605 through 615 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.731A pdb=" N MET B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 641 through 655 removed outlier: 4.687A pdb=" N ARG B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 731 through 737 removed outlier: 3.715A pdb=" N GLN B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 531 through 533 removed outlier: 3.909A pdb=" N ILE A 692 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 501 through 505 removed outlier: 5.310A pdb=" N VAL A 521 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 708 through 710 removed outlier: 6.770A pdb=" N ASP A 710 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.853A pdb=" N LEU B 560 " --> pdb=" O ASP B 501 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 558 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 707 through 709 removed outlier: 3.819A pdb=" N VAL B 707 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 534 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 692 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 660 " --> pdb=" O THR B 689 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1269 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: 2.92 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2486 1.33 - 1.45: 1498 1.45 - 1.57: 4921 1.57 - 1.69: 2 1.69 - 1.81: 72 Bond restraints: 8979 Sorted by residual: bond pdb=" CA ARG B 284 " pdb=" C ARG B 284 " ideal model delta sigma weight residual 1.522 1.431 0.091 1.72e-02 3.38e+03 2.81e+01 bond pdb=" N LEU A 729 " pdb=" CA LEU A 729 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" O4P PGT A 801 " pdb=" P PGT A 801 " ideal model delta sigma weight residual 1.641 1.581 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" CB ASN A 254 " pdb=" CG ASN A 254 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ASN B 254 " pdb=" CG ASN B 254 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.44e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.83: 143 105.83 - 112.87: 4965 112.87 - 119.91: 3212 119.91 - 126.95: 3775 126.95 - 133.99: 66 Bond angle restraints: 12161 Sorted by residual: angle pdb=" C GLY A 728 " pdb=" N LEU A 729 " pdb=" CA LEU A 729 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLN A 298 " pdb=" N ASN A 299 " pdb=" CA ASN A 299 " ideal model delta sigma weight residual 121.52 114.86 6.66 1.84e+00 2.95e-01 1.31e+01 angle pdb=" C VAL B 228 " pdb=" N CYS B 229 " pdb=" CA CYS B 229 " ideal model delta sigma weight residual 121.54 115.03 6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA ARG B 284 " pdb=" C ARG B 284 " pdb=" N LEU B 285 " ideal model delta sigma weight residual 118.59 123.64 -5.05 1.63e+00 3.76e-01 9.59e+00 angle pdb=" C PHE B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 120.72 115.55 5.17 1.67e+00 3.59e-01 9.57e+00 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 5150 30.18 - 60.35: 197 60.35 - 90.53: 21 90.53 - 120.71: 0 120.71 - 150.88: 1 Dihedral angle restraints: 5369 sinusoidal: 2081 harmonic: 3288 Sorted by residual: dihedral pdb=" CA MET B 218 " pdb=" C MET B 218 " pdb=" N ASP B 219 " pdb=" CA ASP B 219 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA MET A 218 " pdb=" C MET A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ILE A 596 " pdb=" C ILE A 596 " pdb=" N SER A 597 " pdb=" CA SER A 597 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 934 0.047 - 0.094: 380 0.094 - 0.141: 93 0.141 - 0.188: 20 0.188 - 0.235: 4 Chirality restraints: 1431 Sorted by residual: chirality pdb=" C5 PGT A 801 " pdb=" C4 PGT A 801 " pdb=" C6 PGT A 801 " pdb=" O5 PGT A 801 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2 PGT A 801 " pdb=" C1 PGT A 801 " pdb=" C3 PGT A 801 " pdb=" O2 PGT A 801 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL B 266 " pdb=" CA VAL B 266 " pdb=" CG1 VAL B 266 " pdb=" CG2 VAL B 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1428 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 296 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C VAL A 296 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 296 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 297 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 178 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 179 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 229 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C CYS B 229 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS B 229 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 230 " 0.017 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1619 2.75 - 3.29: 9100 3.29 - 3.83: 14208 3.83 - 4.36: 15772 4.36 - 4.90: 27016 Nonbonded interactions: 67715 Sorted by model distance: nonbonded pdb=" O ARG A 651 " pdb=" NH1 ARG A 655 " model vdw 2.215 2.520 nonbonded pdb=" O SER A 433 " pdb=" OG SER A 433 " model vdw 2.239 2.440 nonbonded pdb=" O PRO B 493 " pdb=" OH TYR B 573 " model vdw 2.251 2.440 nonbonded pdb=" OG SER B 640 " pdb=" OE1 GLN B 643 " model vdw 2.262 2.440 nonbonded pdb=" O ILE B 677 " pdb=" N ILE B 681 " model vdw 2.266 2.520 ... (remaining 67710 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 169 through 669 or (resid 670 through 672 and (name N or n \ ame CA or name C or name O or name CB )) or resid 673 through 677 or (resid 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 3 or (resid 684 and (name N or name CA or name C or name O or name CB )) or resi \ d 685 through 686 or (resid 687 and (name N or name CA or name C or name O or na \ me CB )) or resid 688 through 695 or (resid 696 and (name N or name CA or name C \ or name O or name CB )) or resid 697 through 735 or (resid 736 through 737 and \ (name N or name CA or name C or name O or name CB )) or resid 738)) selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 634 or (resid 635 and (name N \ or name CA or name C or name O or name CB )) or resid 636 through 665 or (resid \ 666 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 734 or (resid 735 through 737 and (name N or name CA or name C or \ name O or name CB )) or resid 738)) } 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: 1.200 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: 0.020 Extract box with map and model: 4.270 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.290 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:4.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.010 0.091 8979 Z= 0.667 Angle : 0.937 8.109 12161 Z= 0.508 Chirality : 0.054 0.235 1431 Planarity : 0.006 0.073 1541 Dihedral : 16.059 150.884 3261 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.63 % Allowed : 13.28 % Favored : 86.09 % 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: -2.76 (0.23), residues: 1136 helix: -0.95 (0.17), residues: 724 sheet: -4.49 (0.49), residues: 34 loop : -3.20 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 322 HIS 0.007 0.001 HIS A 429 PHE 0.027 0.003 PHE B 272 TYR 0.018 0.002 TYR A 509 ARG 0.023 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.910 Fit side-chains REVERT: A 607 MET cc_start: 0.6627 (mmm) cc_final: 0.6316 (mmm) REVERT: A 616 ASN cc_start: 0.9056 (m-40) cc_final: 0.8619 (t0) REVERT: A 664 GLU cc_start: 0.7539 (pp20) cc_final: 0.7283 (pp20) REVERT: A 721 GLN cc_start: 0.8008 (pp30) cc_final: 0.7740 (pm20) REVERT: B 375 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8375 (mmt180) REVERT: B 456 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 462 TYR cc_start: 0.8218 (t80) cc_final: 0.7853 (t80) REVERT: B 607 MET cc_start: 0.8628 (mpp) cc_final: 0.8390 (mpp) REVERT: B 713 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7310 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.1924 time to fit residues: 34.4492 Evaluate side-chains 94 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 306 ASN A 520 ASN A 618 HIS A 625 GLN A 678 GLN A 679 GLN ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 695 HIS B 716 GLN B 720 HIS B 721 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8979 Z= 0.154 Angle : 0.526 8.071 12161 Z= 0.280 Chirality : 0.038 0.158 1431 Planarity : 0.005 0.053 1541 Dihedral : 7.857 131.309 1288 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.11 % Allowed : 17.60 % Favored : 80.30 % 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 (0.25), residues: 1136 helix: 0.63 (0.20), residues: 716 sheet: -3.99 (0.53), residues: 46 loop : -2.75 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 322 HIS 0.002 0.001 HIS B 487 PHE 0.013 0.001 PHE B 250 TYR 0.020 0.001 TYR A 730 ARG 0.005 0.000 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 466 MET cc_start: 0.7914 (tpp) cc_final: 0.7110 (tpp) REVERT: A 607 MET cc_start: 0.6602 (mmm) cc_final: 0.6316 (mmm) REVERT: A 616 ASN cc_start: 0.9002 (m-40) cc_final: 0.8549 (t0) REVERT: A 721 GLN cc_start: 0.8027 (pp30) cc_final: 0.7763 (pm20) REVERT: B 375 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8133 (mmt180) REVERT: B 653 LEU cc_start: 0.8751 (mt) cc_final: 0.8467 (mt) REVERT: B 713 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7332 (ptp90) outliers start: 20 outliers final: 9 residues processed: 127 average time/residue: 0.2034 time to fit residues: 36.2802 Evaluate side-chains 101 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 GLN ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 GLN B 695 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8979 Z= 0.220 Angle : 0.546 8.145 12161 Z= 0.285 Chirality : 0.040 0.153 1431 Planarity : 0.004 0.042 1541 Dihedral : 7.792 133.198 1285 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.06 % Allowed : 20.65 % Favored : 76.29 % 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: -0.74 (0.26), residues: 1136 helix: 0.74 (0.20), residues: 728 sheet: -3.85 (0.51), residues: 50 loop : -2.57 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.004 0.001 HIS A 429 PHE 0.014 0.001 PHE B 250 TYR 0.013 0.001 TYR A 730 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.6657 (mmm) cc_final: 0.6375 (mmm) REVERT: A 616 ASN cc_start: 0.9007 (m-40) cc_final: 0.8570 (t0) REVERT: A 721 GLN cc_start: 0.8064 (pp30) cc_final: 0.7801 (pm20) REVERT: B 375 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8354 (mmt180) REVERT: B 496 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.5262 (mm) REVERT: B 713 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7322 (ptp90) outliers start: 29 outliers final: 24 residues processed: 115 average time/residue: 0.1869 time to fit residues: 31.0879 Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 707 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 420 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8979 Z= 0.288 Angle : 0.574 6.511 12161 Z= 0.300 Chirality : 0.041 0.147 1431 Planarity : 0.004 0.041 1541 Dihedral : 7.842 133.177 1285 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.95 % Allowed : 20.86 % Favored : 74.18 % 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: -0.74 (0.26), residues: 1136 helix: 0.73 (0.20), residues: 728 sheet: -3.81 (0.45), residues: 68 loop : -2.43 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 322 HIS 0.005 0.001 HIS A 429 PHE 0.016 0.001 PHE B 272 TYR 0.013 0.001 TYR A 730 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 92 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.6664 (mmm) cc_final: 0.6383 (mmm) REVERT: A 616 ASN cc_start: 0.9021 (m-40) cc_final: 0.8550 (t0) REVERT: A 721 GLN cc_start: 0.8000 (pp30) cc_final: 0.7729 (pp30) REVERT: B 375 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8263 (mmt180) REVERT: B 496 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5203 (mm) REVERT: B 713 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7251 (ptp-110) outliers start: 47 outliers final: 36 residues processed: 124 average time/residue: 0.1728 time to fit residues: 31.8628 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 420 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN B 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8979 Z= 0.145 Angle : 0.497 7.530 12161 Z= 0.256 Chirality : 0.038 0.151 1431 Planarity : 0.004 0.046 1541 Dihedral : 7.608 131.589 1285 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 23.92 % Favored : 73.23 % 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: -0.23 (0.26), residues: 1136 helix: 1.19 (0.20), residues: 732 sheet: -3.46 (0.50), residues: 68 loop : -2.47 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 322 HIS 0.002 0.000 HIS A 429 PHE 0.016 0.001 PHE B 250 TYR 0.010 0.001 TYR A 730 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.9053 (tpp) cc_final: 0.8642 (tpp) REVERT: A 616 ASN cc_start: 0.9001 (m-40) cc_final: 0.8581 (t0) REVERT: A 721 GLN cc_start: 0.7778 (pp30) cc_final: 0.7435 (pm20) REVERT: B 375 ARG cc_start: 0.8577 (mmm160) cc_final: 0.8146 (mmt180) REVERT: B 496 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5279 (mm) REVERT: B 713 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7297 (ptp90) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.1959 time to fit residues: 35.7665 Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8979 Z= 0.150 Angle : 0.491 6.885 12161 Z= 0.252 Chirality : 0.038 0.158 1431 Planarity : 0.004 0.035 1541 Dihedral : 7.531 131.791 1285 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.95 % Allowed : 24.55 % Favored : 72.50 % 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: -0.05 (0.27), residues: 1136 helix: 1.32 (0.20), residues: 730 sheet: -3.16 (0.53), residues: 68 loop : -2.40 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 322 HIS 0.003 0.001 HIS B 618 PHE 0.016 0.001 PHE B 250 TYR 0.013 0.001 TYR B 462 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.9003 (m-40) cc_final: 0.8584 (t0) REVERT: B 347 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8538 (mttm) REVERT: B 375 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8208 (mmt180) REVERT: B 401 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 653 LEU cc_start: 0.8877 (mt) cc_final: 0.8616 (mt) REVERT: B 662 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7914 (mt) REVERT: B 713 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7310 (ptp90) outliers start: 28 outliers final: 23 residues processed: 124 average time/residue: 0.1937 time to fit residues: 34.3062 Evaluate side-chains 119 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8979 Z= 0.161 Angle : 0.502 7.506 12161 Z= 0.255 Chirality : 0.038 0.156 1431 Planarity : 0.003 0.031 1541 Dihedral : 7.485 131.339 1285 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.58 % Allowed : 23.92 % Favored : 72.50 % 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: 0.06 (0.27), residues: 1136 helix: 1.37 (0.20), residues: 728 sheet: -2.90 (0.55), residues: 68 loop : -2.32 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.002 0.000 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.012 0.001 TYR A 730 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.6095 (mmm) cc_final: 0.5775 (mmm) REVERT: A 616 ASN cc_start: 0.9005 (m-40) cc_final: 0.8626 (t0) REVERT: B 347 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8532 (mttm) REVERT: B 375 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8227 (mmt180) REVERT: B 401 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 653 LEU cc_start: 0.8874 (mt) cc_final: 0.8603 (mt) REVERT: B 662 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 713 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7297 (ptp90) outliers start: 34 outliers final: 29 residues processed: 120 average time/residue: 0.1926 time to fit residues: 33.0466 Evaluate side-chains 121 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 420 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8979 Z= 0.244 Angle : 0.558 11.670 12161 Z= 0.285 Chirality : 0.040 0.155 1431 Planarity : 0.004 0.031 1541 Dihedral : 7.604 131.997 1285 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.00 % Allowed : 23.39 % Favored : 72.60 % 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: -0.06 (0.26), residues: 1136 helix: 1.17 (0.20), residues: 726 sheet: -2.81 (0.56), residues: 68 loop : -2.07 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.004 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.013 0.001 TYR A 730 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7613 (tp30) cc_final: 0.7194 (mm-30) REVERT: A 466 MET cc_start: 0.7518 (tpp) cc_final: 0.6625 (tpp) REVERT: A 616 ASN cc_start: 0.8995 (m-40) cc_final: 0.8622 (t0) REVERT: B 198 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 347 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8544 (mttm) REVERT: B 375 ARG cc_start: 0.8608 (mmm160) cc_final: 0.8319 (mmt180) REVERT: B 653 LEU cc_start: 0.8860 (mt) cc_final: 0.8608 (mt) REVERT: B 713 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7271 (ptp-110) outliers start: 38 outliers final: 35 residues processed: 118 average time/residue: 0.1881 time to fit residues: 32.2330 Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8979 Z= 0.167 Angle : 0.516 7.629 12161 Z= 0.264 Chirality : 0.038 0.156 1431 Planarity : 0.003 0.032 1541 Dihedral : 7.533 131.274 1285 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.69 % Allowed : 24.13 % Favored : 72.18 % 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: 0.07 (0.27), residues: 1136 helix: 1.25 (0.20), residues: 740 sheet: -2.61 (0.58), residues: 68 loop : -2.16 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.002 0.000 HIS A 429 PHE 0.016 0.001 PHE B 250 TYR 0.013 0.001 TYR A 730 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7517 (tp30) cc_final: 0.7136 (mm-30) REVERT: A 466 MET cc_start: 0.7548 (tpp) cc_final: 0.6734 (tpp) REVERT: A 607 MET cc_start: 0.6043 (mmm) cc_final: 0.5731 (mmm) REVERT: A 616 ASN cc_start: 0.8966 (m-40) cc_final: 0.8607 (t0) REVERT: B 347 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8523 (mttm) REVERT: B 375 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8267 (mmt180) REVERT: B 401 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 653 LEU cc_start: 0.8896 (mt) cc_final: 0.8621 (mt) REVERT: B 662 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7711 (mt) REVERT: B 713 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7303 (ptp90) outliers start: 35 outliers final: 31 residues processed: 119 average time/residue: 0.2015 time to fit residues: 34.1011 Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8979 Z= 0.176 Angle : 0.534 12.959 12161 Z= 0.269 Chirality : 0.038 0.156 1431 Planarity : 0.003 0.032 1541 Dihedral : 7.547 131.844 1285 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.69 % Allowed : 24.45 % Favored : 71.87 % 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: 0.12 (0.26), residues: 1136 helix: 1.27 (0.20), residues: 740 sheet: -2.52 (0.59), residues: 68 loop : -2.11 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.003 0.000 HIS A 429 PHE 0.016 0.001 PHE B 250 TYR 0.014 0.001 TYR A 730 ARG 0.003 0.000 ARG B 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7423 (tp30) cc_final: 0.7029 (mm-30) REVERT: A 466 MET cc_start: 0.7610 (tpp) cc_final: 0.6792 (tpp) REVERT: A 607 MET cc_start: 0.6071 (mmm) cc_final: 0.5761 (mmm) REVERT: A 616 ASN cc_start: 0.8968 (m-40) cc_final: 0.8610 (t0) REVERT: B 347 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8523 (mttm) REVERT: B 401 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 653 LEU cc_start: 0.8903 (mt) cc_final: 0.8631 (mt) REVERT: B 662 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7792 (mt) REVERT: B 713 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7303 (ptp90) outliers start: 35 outliers final: 33 residues processed: 115 average time/residue: 0.1912 time to fit residues: 31.4120 Evaluate side-chains 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110028 restraints weight = 13793.774| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.15 r_work: 0.3441 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8979 Z= 0.195 Angle : 0.526 7.704 12161 Z= 0.270 Chirality : 0.039 0.155 1431 Planarity : 0.003 0.034 1541 Dihedral : 7.366 131.821 1285 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.90 % Allowed : 24.24 % Favored : 71.87 % 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: 0.15 (0.26), residues: 1136 helix: 1.28 (0.20), residues: 726 sheet: -2.45 (0.61), residues: 68 loop : -1.93 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.014 0.001 TYR A 730 ARG 0.003 0.000 ARG B 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.25 seconds wall clock time: 36 minutes 47.51 seconds (2207.51 seconds total)