Starting phenix.real_space_refine on Mon Mar 11 09:45:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpj_24616/03_2024/7rpj_24616.pdb" } resolution = 3.2 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= -0.136 sd= 0.580 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 64 5.16 5 C 5277 2.51 5 N 1188 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 223": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7926 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 945, 7918 Unusual residues: {'NAG': 5, 'Y01': 14} Classifications: {'peptide': 926, 'undetermined': 19} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 19} Not linked: pdbres="PHE A1143 " pdbres="NAG A1601 " Not linked: pdbres="NAG A1601 " pdbres="NAG A1602 " Not linked: pdbres="NAG A1602 " pdbres="NAG A1603 " Not linked: pdbres="NAG A1603 " pdbres="NAG A1604 " Not linked: pdbres="NAG A1604 " pdbres="NAG A1605 " ... (remaining 14 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 945, 7918 Unusual residues: {'NAG': 5, 'Y01': 14} Classifications: {'peptide': 926, 'undetermined': 19} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 19} Not linked: pdbres="PHE A1143 " pdbres="NAG A1601 " Not linked: pdbres="NAG A1601 " pdbres="NAG A1602 " Not linked: pdbres="NAG A1602 " pdbres="NAG A1603 " Not linked: pdbres="NAG A1603 " pdbres="NAG A1604 " Not linked: pdbres="NAG A1604 " pdbres="NAG A1605 " ... (remaining 14 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 8149 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU A1035 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A1035 " occ=0.50 Time building chain proxies: 8.05, per 1000 atoms: 1.02 Number of scatterers: 7926 At special positions: 0 Unit cell: (86.736, 87.57, 124.266, 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 64 16.00 O 1397 8.00 N 1188 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.02 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A1127 " - pdb=" SG CYS A1131 " distance=2.10 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 Links applied NAG-ASN " NAG A1601 " - " ASN A 475 " " NAG A1602 " - " ASN A 834 " " NAG A1603 " - " ASN A 915 " " NAG A1604 " - " ASN A 390 " " NAG A1605 " - " ASN A 362 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 2.6 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 67.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.777A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 243 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.754A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.927A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 391 removed outlier: 5.264A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.065A pdb=" N LYS A 419 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.913A pdb=" N GLN A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 524 through 547 removed outlier: 3.776A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 587 removed outlier: 4.125A pdb=" N THR A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 5.076A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 626 through 662 removed outlier: 4.331A pdb=" N LEU A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 682 through 706 removed outlier: 4.109A pdb=" N CYS A 686 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.847A pdb=" N TYR A 762 " --> pdb=" O PRO A 758 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 818 through 835 removed outlier: 3.594A pdb=" N GLN A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 861 removed outlier: 3.910A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 895 removed outlier: 4.268A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.635A pdb=" N SER A 954 " --> pdb=" O SER A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 963 removed outlier: 3.914A pdb=" N ARG A 962 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 963 " --> pdb=" O LEU A 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 959 through 963' Processing helix chain 'A' and resid 969 through 1002 removed outlier: 3.626A pdb=" N ASP A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 4.386A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1095 removed outlier: 5.364A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.452A pdb=" N GLY A1139 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 451 through 458 removed outlier: 4.231A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.521A pdb=" N ALA A 920 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 783 " --> pdb=" O SER A 927 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1308 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: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1387 1.32 - 1.45: 2290 1.45 - 1.58: 4389 1.58 - 1.71: 5 1.71 - 1.84: 96 Bond restraints: 8167 Sorted by residual: bond pdb=" CA TYR A 245 " pdb=" C TYR A 245 " ideal model delta sigma weight residual 1.528 1.578 -0.051 8.80e-03 1.29e+04 3.32e+01 bond pdb=" N ARG A 225 " pdb=" CA ARG A 225 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.24e-02 6.50e+03 1.63e+01 bond pdb=" C5 NAG A1605 " pdb=" O5 NAG A1605 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG A1604 " pdb=" O5 NAG A1604 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 NAG A1603 " pdb=" O5 NAG A1603 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 8162 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.95: 309 105.95 - 113.23: 4385 113.23 - 120.51: 3892 120.51 - 127.80: 2525 127.80 - 135.08: 76 Bond angle restraints: 11187 Sorted by residual: angle pdb=" N GLY A 394 " pdb=" CA GLY A 394 " pdb=" C GLY A 394 " ideal model delta sigma weight residual 112.00 120.19 -8.19 1.20e+00 6.94e-01 4.66e+01 angle pdb=" C TYR A 869 " pdb=" N PRO A 870 " pdb=" CA PRO A 870 " ideal model delta sigma weight residual 119.56 113.30 6.26 1.01e+00 9.80e-01 3.85e+01 angle pdb=" N ASP A 916 " pdb=" CA ASP A 916 " pdb=" C ASP A 916 " ideal model delta sigma weight residual 111.90 119.33 -7.43 1.32e+00 5.74e-01 3.16e+01 angle pdb=" N CYS A1127 " pdb=" CA CYS A1127 " pdb=" CB CYS A1127 " ideal model delta sigma weight residual 109.91 117.28 -7.37 1.46e+00 4.69e-01 2.55e+01 angle pdb=" CB HIS A 332 " pdb=" CG HIS A 332 " pdb=" CD2 HIS A 332 " ideal model delta sigma weight residual 131.20 124.70 6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 11182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4992 16.83 - 33.65: 419 33.65 - 50.48: 116 50.48 - 67.30: 24 67.30 - 84.13: 6 Dihedral angle restraints: 5557 sinusoidal: 2829 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 177.13 -84.13 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" C ASP A 916 " pdb=" N ASP A 916 " pdb=" CA ASP A 916 " pdb=" CB ASP A 916 " ideal model delta harmonic sigma weight residual -122.60 -138.31 15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N ASP A 478 " pdb=" CA ASP A 478 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 5554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1236 0.193 - 0.385: 66 0.385 - 0.578: 2 0.578 - 0.770: 1 0.770 - 0.963: 1 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C1 NAG A1604 " pdb=" ND2 ASN A 390 " pdb=" C2 NAG A1604 " pdb=" O5 NAG A1604 " both_signs ideal model delta sigma weight residual False -2.40 -3.36 0.96 2.00e-01 2.50e+01 2.32e+01 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA LYS A 522 " pdb=" N LYS A 522 " pdb=" C LYS A 522 " pdb=" CB LYS A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 1303 not shown) Planarity restraints: 1321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 362 " -0.136 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN A 362 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 362 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 362 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG A1605 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1030 " 0.133 2.00e-02 2.50e+03 7.56e-02 1.43e+02 pdb=" CG TRP A1030 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A1030 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A1030 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A1030 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP A1030 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1030 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1030 " 0.094 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1030 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP A1030 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 283 " 0.124 2.00e-02 2.50e+03 6.86e-02 1.18e+02 pdb=" CG TRP A 283 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 283 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 283 " -0.098 2.00e-02 2.50e+03 pdb=" NE1 TRP A 283 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 283 " -0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 283 " -0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 283 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 283 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 283 " 0.085 2.00e-02 2.50e+03 ... (remaining 1318 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3763 2.95 - 3.43: 8917 3.43 - 3.92: 13016 3.92 - 4.41: 15341 4.41 - 4.90: 24375 Nonbonded interactions: 65412 Sorted by model distance: nonbonded pdb=" OD1 ASP A 896 " pdb=" NE2 HIS A 902 " model vdw 2.458 2.520 nonbonded pdb=" O THR A 392 " pdb=" N CYS A 410 " model vdw 2.557 2.520 nonbonded pdb=" OD1 ASP A 845 " pdb=" OG1 THR A 847 " model vdw 2.559 2.440 nonbonded pdb=" O VAL A1113 " pdb=" OG SER A1117 " model vdw 2.560 2.440 nonbonded pdb=" O PHE A 694 " pdb=" OG SER A 697 " model vdw 2.564 2.440 ... (remaining 65407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.560 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: 5.280 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.810 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 : 0.014 0.078 8167 Z= 0.868 Angle : 1.718 11.678 11187 Z= 1.114 Chirality : 0.105 0.963 1306 Planarity : 0.014 0.130 1316 Dihedral : 13.324 77.694 3764 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 0.98 % Allowed : 5.41 % Favored : 93.61 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.50 % 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: -1.66 (0.26), residues: 921 helix: -0.99 (0.19), residues: 557 sheet: -0.48 (0.95), residues: 29 loop : -1.06 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.025 TRP A1030 HIS 0.010 0.004 HIS A 782 PHE 0.100 0.014 PHE A 850 TYR 0.112 0.018 TYR A 942 ARG 0.011 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7291 (ttp) cc_final: 0.7047 (ttt) REVERT: A 211 GLU cc_start: 0.8630 (pm20) cc_final: 0.7854 (tp30) REVERT: A 369 ILE cc_start: 0.8712 (pt) cc_final: 0.8477 (mt) REVERT: A 448 LEU cc_start: 0.8654 (tp) cc_final: 0.8421 (tp) REVERT: A 449 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8485 (ttpp) REVERT: A 529 MET cc_start: 0.7455 (mmt) cc_final: 0.6703 (mmm) REVERT: A 647 MET cc_start: 0.7925 (mmt) cc_final: 0.7620 (mmm) REVERT: A 776 HIS cc_start: 0.8141 (t-90) cc_final: 0.7834 (t70) REVERT: A 794 GLU cc_start: 0.8533 (tt0) cc_final: 0.7836 (mp0) REVERT: A 869 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: A 940 GLN cc_start: 0.8865 (tt0) cc_final: 0.8651 (tp-100) REVERT: A 965 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 1047 SER cc_start: 0.8335 (t) cc_final: 0.7918 (m) REVERT: A 1111 MET cc_start: 0.6999 (mtm) cc_final: 0.6652 (mtm) REVERT: A 1128 LEU cc_start: 0.8676 (mp) cc_final: 0.8458 (mp) outliers start: 7 outliers final: 2 residues processed: 137 average time/residue: 0.1984 time to fit residues: 37.2111 Evaluate side-chains 80 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 687 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 8167 Z= 0.247 Angle : 0.741 16.350 11187 Z= 0.363 Chirality : 0.044 0.219 1306 Planarity : 0.004 0.041 1316 Dihedral : 9.891 59.534 2102 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 11.30 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 921 helix: 0.86 (0.21), residues: 571 sheet: 0.12 (0.94), residues: 29 loop : -0.38 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 789 HIS 0.005 0.001 HIS A 827 PHE 0.015 0.001 PHE A 618 TYR 0.018 0.002 TYR A1009 ARG 0.006 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7404 (ttp) cc_final: 0.7178 (ttp) REVERT: A 211 GLU cc_start: 0.8652 (pm20) cc_final: 0.7824 (tp30) REVERT: A 217 ASP cc_start: 0.8155 (t70) cc_final: 0.7785 (t70) REVERT: A 431 VAL cc_start: 0.8852 (t) cc_final: 0.8622 (p) REVERT: A 449 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8529 (ttpp) REVERT: A 524 MET cc_start: 0.6934 (ptp) cc_final: 0.6420 (ptt) REVERT: A 529 MET cc_start: 0.7596 (mmt) cc_final: 0.6666 (mmm) REVERT: A 582 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6161 (t80) REVERT: A 776 HIS cc_start: 0.8259 (t-90) cc_final: 0.8038 (t70) REVERT: A 794 GLU cc_start: 0.8450 (tt0) cc_final: 0.8243 (tt0) REVERT: A 869 TYR cc_start: 0.8922 (p90) cc_final: 0.8566 (m-10) REVERT: A 1047 SER cc_start: 0.8501 (t) cc_final: 0.7909 (m) REVERT: A 1083 MET cc_start: 0.7320 (mmp) cc_final: 0.6998 (tpp) REVERT: A 1128 LEU cc_start: 0.8362 (mp) cc_final: 0.8151 (mp) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.1635 time to fit residues: 26.7493 Evaluate side-chains 81 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1127 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.6539 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8167 Z= 0.270 Angle : 0.691 11.140 11187 Z= 0.333 Chirality : 0.042 0.223 1306 Planarity : 0.004 0.041 1316 Dihedral : 9.673 59.931 2096 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.33 % Allowed : 13.14 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.08 (0.28), residues: 921 helix: 1.29 (0.22), residues: 562 sheet: 0.38 (0.99), residues: 29 loop : -0.13 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 789 HIS 0.005 0.001 HIS A1053 PHE 0.015 0.001 PHE A 618 TYR 0.013 0.002 TYR A 869 ARG 0.007 0.001 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7306 (ttp) cc_final: 0.7098 (ttt) REVERT: A 211 GLU cc_start: 0.8547 (pm20) cc_final: 0.7876 (tp30) REVERT: A 217 ASP cc_start: 0.8113 (t70) cc_final: 0.7703 (t70) REVERT: A 348 CYS cc_start: 0.7548 (t) cc_final: 0.6130 (p) REVERT: A 431 VAL cc_start: 0.8912 (t) cc_final: 0.8668 (p) REVERT: A 449 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8526 (ttpp) REVERT: A 529 MET cc_start: 0.7598 (mmt) cc_final: 0.6713 (mmm) REVERT: A 582 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6019 (t80) REVERT: A 693 LEU cc_start: 0.9255 (mp) cc_final: 0.8830 (pp) REVERT: A 776 HIS cc_start: 0.8288 (t-90) cc_final: 0.8064 (t70) REVERT: A 794 GLU cc_start: 0.8435 (tt0) cc_final: 0.8174 (tt0) REVERT: A 1047 SER cc_start: 0.8374 (t) cc_final: 0.7782 (m) REVERT: A 1131 CYS cc_start: 0.4107 (OUTLIER) cc_final: 0.3626 (t) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.1562 time to fit residues: 24.1285 Evaluate side-chains 92 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1131 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.6495 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8167 Z= 0.176 Angle : 0.637 10.524 11187 Z= 0.306 Chirality : 0.040 0.231 1306 Planarity : 0.004 0.045 1316 Dihedral : 9.242 59.812 2096 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.47 % Allowed : 14.00 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.37 (0.28), residues: 921 helix: 1.55 (0.22), residues: 562 sheet: 0.46 (1.02), residues: 28 loop : -0.07 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 313 HIS 0.003 0.000 HIS A1053 PHE 0.025 0.001 PHE A 435 TYR 0.015 0.001 TYR A 869 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6403 (mt) cc_final: 0.6189 (tp) REVERT: A 211 GLU cc_start: 0.8534 (pm20) cc_final: 0.7689 (tp30) REVERT: A 217 ASP cc_start: 0.8006 (t70) cc_final: 0.7717 (t70) REVERT: A 431 VAL cc_start: 0.8803 (t) cc_final: 0.8535 (p) REVERT: A 449 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8520 (ttpp) REVERT: A 529 MET cc_start: 0.7584 (mmt) cc_final: 0.6634 (mmm) REVERT: A 582 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.6027 (t80) REVERT: A 693 LEU cc_start: 0.9252 (mp) cc_final: 0.8829 (pp) REVERT: A 776 HIS cc_start: 0.8304 (t-90) cc_final: 0.8052 (t70) REVERT: A 794 GLU cc_start: 0.8450 (tt0) cc_final: 0.8191 (tt0) REVERT: A 998 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7118 (mm) REVERT: A 1096 MET cc_start: 0.7942 (mmm) cc_final: 0.7740 (mmm) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.1473 time to fit residues: 22.0937 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8167 Z= 0.204 Angle : 0.619 11.086 11187 Z= 0.298 Chirality : 0.039 0.232 1306 Planarity : 0.004 0.044 1316 Dihedral : 9.122 59.465 2096 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.84 % Allowed : 13.27 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 921 helix: 1.60 (0.22), residues: 564 sheet: 0.36 (1.02), residues: 28 loop : -0.05 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 313 HIS 0.003 0.001 HIS A1053 PHE 0.020 0.001 PHE A 770 TYR 0.014 0.001 TYR A 869 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6410 (mt) cc_final: 0.6188 (tp) REVERT: A 211 GLU cc_start: 0.8498 (pm20) cc_final: 0.7676 (tp30) REVERT: A 217 ASP cc_start: 0.7989 (t70) cc_final: 0.7686 (t70) REVERT: A 431 VAL cc_start: 0.8808 (t) cc_final: 0.8559 (p) REVERT: A 449 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8593 (ttpp) REVERT: A 529 MET cc_start: 0.7569 (mmt) cc_final: 0.6649 (mmm) REVERT: A 582 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.6068 (t80) REVERT: A 693 LEU cc_start: 0.9268 (mp) cc_final: 0.8856 (pp) REVERT: A 776 HIS cc_start: 0.8291 (t-90) cc_final: 0.8014 (t70) REVERT: A 794 GLU cc_start: 0.8452 (tt0) cc_final: 0.8168 (tt0) REVERT: A 846 PHE cc_start: 0.7910 (m-10) cc_final: 0.6889 (p90) REVERT: A 998 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7069 (mm) REVERT: A 1096 MET cc_start: 0.7851 (mmm) cc_final: 0.7574 (mmm) REVERT: A 1110 MET cc_start: 0.6898 (tpp) cc_final: 0.6688 (mmt) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.1454 time to fit residues: 21.0114 Evaluate side-chains 92 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8167 Z= 0.167 Angle : 0.584 11.501 11187 Z= 0.284 Chirality : 0.039 0.238 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.764 58.843 2096 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.84 % Allowed : 12.65 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 921 helix: 1.69 (0.22), residues: 569 sheet: 0.29 (1.04), residues: 28 loop : -0.07 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 948 HIS 0.003 0.001 HIS A1053 PHE 0.014 0.001 PHE A 435 TYR 0.014 0.001 TYR A 869 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6377 (mt) cc_final: 0.6132 (tp) REVERT: A 211 GLU cc_start: 0.8428 (pm20) cc_final: 0.7628 (tp30) REVERT: A 212 LEU cc_start: 0.8846 (mt) cc_final: 0.7933 (mp) REVERT: A 217 ASP cc_start: 0.7900 (t70) cc_final: 0.7600 (t70) REVERT: A 449 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8589 (ttpp) REVERT: A 464 MET cc_start: 0.8418 (mmt) cc_final: 0.8181 (mmt) REVERT: A 529 MET cc_start: 0.7572 (mmt) cc_final: 0.6655 (mmm) REVERT: A 582 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5932 (t80) REVERT: A 693 LEU cc_start: 0.9263 (mp) cc_final: 0.8843 (pp) REVERT: A 776 HIS cc_start: 0.8311 (t-90) cc_final: 0.8024 (t70) REVERT: A 794 GLU cc_start: 0.8477 (tt0) cc_final: 0.8198 (tt0) REVERT: A 846 PHE cc_start: 0.7908 (m-10) cc_final: 0.6925 (p90) REVERT: A 998 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 1083 MET cc_start: 0.7105 (tpp) cc_final: 0.6771 (tpp) REVERT: A 1096 MET cc_start: 0.7928 (mmm) cc_final: 0.7683 (mmm) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.1513 time to fit residues: 22.3817 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6495 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8167 Z= 0.178 Angle : 0.577 12.161 11187 Z= 0.283 Chirality : 0.039 0.239 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.660 59.616 2094 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.60 % Allowed : 12.78 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.51 (0.28), residues: 921 helix: 1.72 (0.22), residues: 569 sheet: 0.22 (1.03), residues: 28 loop : -0.14 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 948 HIS 0.002 0.001 HIS A1053 PHE 0.016 0.001 PHE A 435 TYR 0.019 0.001 TYR A 388 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6320 (mt) cc_final: 0.6083 (tp) REVERT: A 211 GLU cc_start: 0.8409 (pm20) cc_final: 0.7617 (tp30) REVERT: A 212 LEU cc_start: 0.8863 (mt) cc_final: 0.7945 (mp) REVERT: A 217 ASP cc_start: 0.7939 (t70) cc_final: 0.7636 (t70) REVERT: A 432 ASP cc_start: 0.8209 (t0) cc_final: 0.7981 (t0) REVERT: A 449 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8613 (ttpp) REVERT: A 529 MET cc_start: 0.7624 (mmt) cc_final: 0.6664 (mmm) REVERT: A 582 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5924 (t80) REVERT: A 693 LEU cc_start: 0.9265 (mp) cc_final: 0.8840 (pp) REVERT: A 776 HIS cc_start: 0.8301 (t-90) cc_final: 0.7975 (t70) REVERT: A 794 GLU cc_start: 0.8456 (tt0) cc_final: 0.8186 (tt0) REVERT: A 846 PHE cc_start: 0.7939 (m-10) cc_final: 0.6943 (p90) REVERT: A 1083 MET cc_start: 0.7117 (tpp) cc_final: 0.6766 (tpp) REVERT: A 1096 MET cc_start: 0.7849 (mmm) cc_final: 0.7611 (mmm) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1605 time to fit residues: 22.8215 Evaluate side-chains 91 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8167 Z= 0.171 Angle : 0.580 11.932 11187 Z= 0.281 Chirality : 0.039 0.240 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.544 58.936 2094 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 13.14 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.58 (0.28), residues: 921 helix: 1.81 (0.22), residues: 566 sheet: 0.21 (1.04), residues: 28 loop : -0.16 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 650 HIS 0.003 0.001 HIS A1053 PHE 0.015 0.001 PHE A 495 TYR 0.014 0.001 TYR A 388 ARG 0.007 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6336 (mt) cc_final: 0.6083 (tp) REVERT: A 211 GLU cc_start: 0.8391 (pm20) cc_final: 0.7633 (tp30) REVERT: A 212 LEU cc_start: 0.8864 (mt) cc_final: 0.8034 (mp) REVERT: A 217 ASP cc_start: 0.7927 (t70) cc_final: 0.7615 (t70) REVERT: A 432 ASP cc_start: 0.8198 (t0) cc_final: 0.7953 (t0) REVERT: A 449 LYS cc_start: 0.9004 (mmtm) cc_final: 0.8606 (ttpp) REVERT: A 529 MET cc_start: 0.7555 (mmt) cc_final: 0.6667 (mmm) REVERT: A 582 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5848 (t80) REVERT: A 693 LEU cc_start: 0.9263 (mp) cc_final: 0.8845 (pp) REVERT: A 776 HIS cc_start: 0.8282 (t-90) cc_final: 0.7933 (t70) REVERT: A 794 GLU cc_start: 0.8472 (tt0) cc_final: 0.8190 (tt0) REVERT: A 846 PHE cc_start: 0.7947 (m-10) cc_final: 0.6861 (p90) REVERT: A 1072 PHE cc_start: 0.8581 (t80) cc_final: 0.8337 (t80) REVERT: A 1083 MET cc_start: 0.7175 (tpp) cc_final: 0.6840 (tpp) REVERT: A 1096 MET cc_start: 0.7836 (mmm) cc_final: 0.7609 (mmm) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1411 time to fit residues: 20.4450 Evaluate side-chains 90 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 0.0010 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8167 Z= 0.173 Angle : 0.598 14.797 11187 Z= 0.285 Chirality : 0.039 0.239 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.458 58.036 2094 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.35 % Allowed : 13.64 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 921 helix: 1.82 (0.22), residues: 567 sheet: 0.01 (1.02), residues: 28 loop : -0.29 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 PHE 0.016 0.001 PHE A 495 TYR 0.013 0.001 TYR A 388 ARG 0.007 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6351 (mt) cc_final: 0.6120 (tp) REVERT: A 211 GLU cc_start: 0.8371 (pm20) cc_final: 0.7612 (tp30) REVERT: A 212 LEU cc_start: 0.8864 (mt) cc_final: 0.8011 (mp) REVERT: A 217 ASP cc_start: 0.7907 (t70) cc_final: 0.7585 (t70) REVERT: A 432 ASP cc_start: 0.8145 (t0) cc_final: 0.7893 (t0) REVERT: A 449 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8600 (ttpp) REVERT: A 529 MET cc_start: 0.7559 (mmt) cc_final: 0.6686 (mmm) REVERT: A 582 TYR cc_start: 0.6261 (OUTLIER) cc_final: 0.5817 (t80) REVERT: A 693 LEU cc_start: 0.9257 (mp) cc_final: 0.8850 (pp) REVERT: A 776 HIS cc_start: 0.8311 (t-90) cc_final: 0.7950 (t70) REVERT: A 794 GLU cc_start: 0.8451 (tt0) cc_final: 0.8177 (tt0) REVERT: A 846 PHE cc_start: 0.7913 (m-10) cc_final: 0.6904 (p90) REVERT: A 998 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7238 (mm) REVERT: A 1096 MET cc_start: 0.7876 (mmm) cc_final: 0.7631 (mmm) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1474 time to fit residues: 21.9005 Evaluate side-chains 93 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8167 Z= 0.191 Angle : 0.609 15.972 11187 Z= 0.291 Chirality : 0.039 0.238 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.474 56.708 2094 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.35 % Allowed : 13.88 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.47 (0.28), residues: 921 helix: 1.78 (0.22), residues: 567 sheet: -0.06 (1.01), residues: 28 loop : -0.32 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 PHE 0.015 0.001 PHE A 495 TYR 0.013 0.001 TYR A 869 ARG 0.008 0.000 ARG A 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6362 (mt) cc_final: 0.6111 (tp) REVERT: A 211 GLU cc_start: 0.8371 (pm20) cc_final: 0.7615 (tp30) REVERT: A 212 LEU cc_start: 0.8870 (mt) cc_final: 0.8007 (mp) REVERT: A 217 ASP cc_start: 0.7924 (t70) cc_final: 0.7606 (t70) REVERT: A 245 TYR cc_start: 0.8013 (t80) cc_final: 0.7752 (t80) REVERT: A 432 ASP cc_start: 0.8191 (t0) cc_final: 0.7931 (t0) REVERT: A 449 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8674 (tttt) REVERT: A 529 MET cc_start: 0.7557 (mmt) cc_final: 0.6700 (mmm) REVERT: A 582 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5842 (t80) REVERT: A 693 LEU cc_start: 0.9258 (mp) cc_final: 0.8853 (pp) REVERT: A 776 HIS cc_start: 0.8310 (t-90) cc_final: 0.7917 (t70) REVERT: A 794 GLU cc_start: 0.8473 (tt0) cc_final: 0.8172 (tt0) REVERT: A 846 PHE cc_start: 0.7966 (m-10) cc_final: 0.6940 (p90) REVERT: A 998 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7180 (mm) REVERT: A 1096 MET cc_start: 0.7786 (mmm) cc_final: 0.7555 (mmm) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.1431 time to fit residues: 20.3040 Evaluate side-chains 95 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.121424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091428 restraints weight = 34158.840| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.15 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8167 Z= 0.162 Angle : 0.588 16.333 11187 Z= 0.282 Chirality : 0.038 0.239 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.325 56.877 2094 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.35 % Allowed : 14.00 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.54 (0.28), residues: 921 helix: 1.84 (0.22), residues: 568 sheet: -0.05 (1.00), residues: 28 loop : -0.29 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 PHE 0.017 0.001 PHE A 495 TYR 0.014 0.001 TYR A 869 ARG 0.007 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.86 seconds wall clock time: 33 minutes 38.30 seconds (2018.30 seconds total)