Starting phenix.real_space_refine on Fri May 16 05:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.map" model { file = "/net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ror_19402/05_2025/8ror_19402.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 27 5.16 5 C 8782 2.51 5 N 2400 2.21 5 O 2996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14205 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 10563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1349, 10472 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 88, 'TRANS': 1258} Chain breaks: 13 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1349, 10472 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 88, 'TRANS': 1258} Chain breaks: 13 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 10629 Chain: "L" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1698 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "H" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain: "1" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 267 Classifications: {'water': 267} Link IDs: {None: 266} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ALYS 1 240 " occ=0.70 ... (16 atoms not shown) pdb=" NZ BLYS 1 240 " occ=0.30 residue: pdb=" N AGLU 1 764 " occ=0.47 ... (16 atoms not shown) pdb=" OE2BGLU 1 764 " occ=0.53 residue: pdb=" N AARG 1 789 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG 1 789 " occ=0.29 residue: pdb=" N APHE 1 850 " occ=0.48 ... (20 atoms not shown) pdb=" CZ BPHE 1 850 " occ=0.52 residue: pdb=" N AASN 1 911 " occ=0.56 ... (14 atoms not shown) pdb=" ND2BASN 1 911 " occ=0.44 residue: pdb=" N ATRP 11025 " occ=0.43 ... (26 atoms not shown) pdb=" CH2BTRP 11025 " occ=0.57 residue: pdb=" N AGLN 11034 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN 11034 " occ=0.48 residue: pdb=" N AARG 11172 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG 11172 " occ=0.33 residue: pdb=" N ALYS 11454 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS 11454 " occ=0.45 Time building chain proxies: 11.94, per 1000 atoms: 0.84 Number of scatterers: 14205 At special positions: 0 Unit cell: (93, 110, 129, 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 27 16.00 O 2996 8.00 N 2400 7.00 C 8782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS H 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 33 sheets defined 20.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain '1' and resid 112 through 124 Processing helix chain '1' and resid 204 through 209 removed outlier: 3.728A pdb=" N VAL 1 208 " --> pdb=" O PRO 1 204 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 214 removed outlier: 3.625A pdb=" N GLN 1 214 " --> pdb=" O GLU 1 211 " (cutoff:3.500A) Processing helix chain '1' and resid 250 through 254 Processing helix chain '1' and resid 328 through 333 Processing helix chain '1' and resid 358 through 364 Processing helix chain '1' and resid 365 through 370 Processing helix chain '1' and resid 395 through 401 Processing helix chain '1' and resid 404 through 409 Processing helix chain '1' and resid 415 through 426 removed outlier: 3.872A pdb=" N ASP 1 419 " --> pdb=" O HIS 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 438 through 442 removed outlier: 3.522A pdb=" N TRP 1 441 " --> pdb=" O HIS 1 438 " (cutoff:3.500A) Processing helix chain '1' and resid 462 through 466 Processing helix chain '1' and resid 483 through 490 Processing helix chain '1' and resid 542 through 547 Processing helix chain '1' and resid 550 through 554 Processing helix chain '1' and resid 611 through 619 Processing helix chain '1' and resid 641 through 645 Processing helix chain '1' and resid 662 through 666 Processing helix chain '1' and resid 670 through 678 Processing helix chain '1' and resid 678 through 683 removed outlier: 4.038A pdb=" N ASP 1 683 " --> pdb=" O LYS 1 679 " (cutoff:3.500A) Processing helix chain '1' and resid 686 through 688 No H-bonds generated for 'chain '1' and resid 686 through 688' Processing helix chain '1' and resid 701 through 710 Processing helix chain '1' and resid 739 through 746 Processing helix chain '1' and resid 761 through 767 Processing helix chain '1' and resid 779 through 785 Proline residue: 1 785 - end of helix Processing helix chain '1' and resid 797 through 808 Processing helix chain '1' and resid 822 through 826 Processing helix chain '1' and resid 867 through 871 Processing helix chain '1' and resid 915 through 919 Processing helix chain '1' and resid 988 through 1001 Processing helix chain '1' and resid 1026 through 1033 removed outlier: 4.108A pdb=" N SER 11032 " --> pdb=" O THR 11028 " (cutoff:3.500A) Processing helix chain '1' and resid 1034 through 1037 Processing helix chain '1' and resid 1049 through 1059 Processing helix chain '1' and resid 1059 through 1067 Processing helix chain '1' and resid 1146 through 1154 Processing helix chain '1' and resid 1179 through 1192 Processing helix chain '1' and resid 1220 through 1223 Processing helix chain '1' and resid 1237 through 1241 removed outlier: 4.526A pdb=" N HIS 11241 " --> pdb=" O PRO 11238 " (cutoff:3.500A) Processing helix chain '1' and resid 1249 through 1253 Processing helix chain '1' and resid 1255 through 1262 Processing helix chain '1' and resid 1263 through 1275 removed outlier: 3.536A pdb=" N VAL 11267 " --> pdb=" O ASP 11263 " (cutoff:3.500A) Processing helix chain '1' and resid 1302 through 1307 Processing helix chain '1' and resid 1326 through 1338 Processing helix chain '1' and resid 1418 through 1423 removed outlier: 4.524A pdb=" N HIS 11423 " --> pdb=" O ARG 11419 " (cutoff:3.500A) Processing helix chain '1' and resid 1424 through 1427 Processing helix chain '1' and resid 1452 through 1454 No H-bonds generated for 'chain '1' and resid 1452 through 1454' Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'H' and resid 55 through 60 removed outlier: 4.741A pdb=" N GLY H 60 " --> pdb=" O GLN H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 Processing sheet with id=AA1, first strand: chain '1' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain '1' and resid 67 through 68 removed outlier: 4.139A pdb=" N TYR 1 139 " --> pdb=" O ARG 1 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain '1' and resid 184 through 190 removed outlier: 6.593A pdb=" N VAL 1 203 " --> pdb=" O PRO 1 185 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU 1 187 " --> pdb=" O LEU 1 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 184 through 190 removed outlier: 6.593A pdb=" N VAL 1 203 " --> pdb=" O PRO 1 185 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU 1 187 " --> pdb=" O LEU 1 201 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA 1 371 " --> pdb=" O LEU 1 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain '1' and resid 257 through 259 removed outlier: 3.924A pdb=" N LYS 1 307 " --> pdb=" O LYS 1 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 257 through 259 Processing sheet with id=AA9, first strand: chain '1' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain '1' and resid 494 through 497 Processing sheet with id=AB2, first strand: chain '1' and resid 574 through 582 removed outlier: 4.684A pdb=" N VAL 1 576 " --> pdb=" O THR 1 591 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR 1 591 " --> pdb=" O VAL 1 576 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY 1 578 " --> pdb=" O ALA 1 589 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL 1 582 " --> pdb=" O GLU 1 585 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU 1 585 " --> pdb=" O VAL 1 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 595 through 596 removed outlier: 4.047A pdb=" N GLU 1 725 " --> pdb=" O ASP 1 596 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 862 through 864 Processing sheet with id=AB5, first strand: chain '1' and resid 913 through 914 Processing sheet with id=AB6, first strand: chain '1' and resid 949 through 953 Processing sheet with id=AB7, first strand: chain '1' and resid 1006 through 1008 Processing sheet with id=AB8, first strand: chain '1' and resid 1010 through 1011 Processing sheet with id=AB9, first strand: chain '1' and resid 1107 through 1109 Processing sheet with id=AC1, first strand: chain '1' and resid 1162 through 1167 removed outlier: 6.184A pdb=" N VAL 11176 " --> pdb=" O ARG 11163 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER 11165 " --> pdb=" O GLU 11174 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU 11174 " --> pdb=" O SER 11165 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1' and resid 1384 through 1386 Processing sheet with id=AC3, first strand: chain '1' and resid 1408 through 1409 Processing sheet with id=AC4, first strand: chain '1' and resid 1429 through 1430 removed outlier: 3.610A pdb=" N LEU 11435 " --> pdb=" O ASP 11430 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU 11458 " --> pdb=" O VAL 11436 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY 11471 " --> pdb=" O LEU 11461 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE 11463 " --> pdb=" O SER 11469 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 11469 " --> pdb=" O PHE 11463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '1' and resid 1429 through 1430 removed outlier: 3.610A pdb=" N LEU 11435 " --> pdb=" O ASP 11430 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU 11458 " --> pdb=" O VAL 11436 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY 11471 " --> pdb=" O LEU 11461 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE 11463 " --> pdb=" O SER 11469 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 11469 " --> pdb=" O PHE 11463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 2 through 4 removed outlier: 3.687A pdb=" N THR L 2 " --> pdb=" O ARG L 21 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 10 removed outlier: 3.772A pdb=" N GLY L 86 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR L 51 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.513A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 155 through 157 removed outlier: 4.341A pdb=" N TRP L 150 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid -3 through 0 removed outlier: 4.018A pdb=" N MET H 12 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid -3 through 0 Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.822A pdb=" N GLU H 4 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET H 28 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU H 44 " --> pdb=" O MET H 28 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP H 30 " --> pdb=" O ILE H 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.822A pdb=" N GLU H 4 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR H 103 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN H 94 " --> pdb=" O MET H 101 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N MET H 101 " --> pdb=" O ASN H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 121 through 125 removed outlier: 6.548A pdb=" N TYR H 176 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 177 " --> pdb=" O VAL H 170 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 152 through 155 445 hydrogen bonds defined for protein. 1126 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: 7.66 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4596 1.34 - 1.46: 3144 1.46 - 1.58: 6508 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 14292 Sorted by residual: bond pdb=" CB GLN 1 323 " pdb=" CG GLN 1 323 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CA ASN 1 182 " pdb=" C ASN 1 182 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.72e-02 3.38e+03 1.95e+00 bond pdb=" CB TRP 1 634 " pdb=" CG TRP 1 634 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.59e+00 bond pdb=" CG LYS 1 749 " pdb=" CD LYS 1 749 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CA ASN 11351 " pdb=" CB ASN 11351 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.42e-02 4.96e+03 1.47e+00 ... (remaining 14287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 19190 2.43 - 4.86: 259 4.86 - 7.28: 28 7.28 - 9.71: 7 9.71 - 12.14: 2 Bond angle restraints: 19486 Sorted by residual: angle pdb=" N VAL 1 448 " pdb=" CA VAL 1 448 " pdb=" C VAL 1 448 " ideal model delta sigma weight residual 112.43 107.28 5.15 9.20e-01 1.18e+00 3.14e+01 angle pdb=" C ASP 1 958 " pdb=" CA ASP 1 958 " pdb=" CB ASP 1 958 " ideal model delta sigma weight residual 116.54 110.35 6.19 1.15e+00 7.56e-01 2.89e+01 angle pdb=" CA GLN 1 323 " pdb=" CB GLN 1 323 " pdb=" CG GLN 1 323 " ideal model delta sigma weight residual 114.10 122.40 -8.30 2.00e+00 2.50e-01 1.72e+01 angle pdb=" CB LYS 1 749 " pdb=" CG LYS 1 749 " pdb=" CD LYS 1 749 " ideal model delta sigma weight residual 111.30 120.62 -9.32 2.30e+00 1.89e-01 1.64e+01 angle pdb=" C MET H 101 " pdb=" N ASP H 102 " pdb=" CA ASP H 102 " ideal model delta sigma weight residual 121.54 129.18 -7.64 1.91e+00 2.74e-01 1.60e+01 ... (remaining 19481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7215 17.97 - 35.94: 933 35.94 - 53.92: 253 53.92 - 71.89: 47 71.89 - 89.86: 29 Dihedral angle restraints: 8477 sinusoidal: 3308 harmonic: 5169 Sorted by residual: dihedral pdb=" CA MET 1 574 " pdb=" C MET 1 574 " pdb=" N ALA 1 575 " pdb=" CA ALA 1 575 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual 93.00 134.01 -41.01 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA TRP 1 634 " pdb=" C TRP 1 634 " pdb=" N ALA 1 635 " pdb=" CA ALA 1 635 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1416 0.036 - 0.072: 492 0.072 - 0.109: 181 0.109 - 0.145: 39 0.145 - 0.181: 3 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA ASN 11351 " pdb=" N ASN 11351 " pdb=" C ASN 11351 " pdb=" CB ASN 11351 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CG LEU 1 501 " pdb=" CB LEU 1 501 " pdb=" CD1 LEU 1 501 " pdb=" CD2 LEU 1 501 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA ILE 1 737 " pdb=" N ILE 1 737 " pdb=" C ILE 1 737 " pdb=" CB ILE 1 737 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 2128 not shown) Planarity restraints: 2557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS 11423 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO 11424 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO 11424 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO 11424 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 1 637 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO 1 638 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 1 638 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO 1 638 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 11514 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO 11515 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO 11515 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO 11515 " -0.030 5.00e-02 4.00e+02 ... (remaining 2554 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 584 2.59 - 3.17: 13545 3.17 - 3.75: 29175 3.75 - 4.32: 40494 4.32 - 4.90: 61955 Nonbonded interactions: 145753 Sorted by model distance: nonbonded pdb=" OH TYR 1 139 " pdb=" OD1 ASP 1 378 " model vdw 2.015 3.040 nonbonded pdb=" O GLN 1 617 " pdb=" OH TYR 1 728 " model vdw 2.060 3.040 nonbonded pdb=" O LYS 1 285 " pdb=" OH TYR 1 657 " model vdw 2.118 3.040 nonbonded pdb=" NZ LYS 11088 " pdb=" O LYS 11253 " model vdw 2.119 3.120 nonbonded pdb=" OG1 THR 1 536 " pdb=" OD2 ASP 1 748 " model vdw 2.148 3.040 ... (remaining 145748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.29 max=1.00 mean=0.99 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: 3.190 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0223 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 : 0.005 0.046 14296 Z= 0.202 Angle : 0.686 12.139 19494 Z= 0.355 Chirality : 0.043 0.181 2131 Planarity : 0.005 0.057 2557 Dihedral : 18.032 89.860 5147 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 3.34 % Allowed : 27.55 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.05 (0.20), residues: 1784 helix: -0.56 (0.30), residues: 266 sheet: -1.74 (0.26), residues: 369 loop : -0.27 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 709 HIS 0.005 0.001 HIS 1 515 PHE 0.023 0.002 PHE 1 488 TYR 0.031 0.002 TYR L 51 ARG 0.009 0.001 ARG 1 136 Details of bonding type rmsd hydrogen bonds : bond 0.17193 ( 415) hydrogen bonds : angle 9.35457 ( 1126) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.46028 ( 8) covalent geometry : bond 0.00462 (14292) covalent geometry : angle 0.68616 (19486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 307 LYS cc_start: 0.3520 (tttm) cc_final: 0.3214 (mmmt) REVERT: 1 1377 MET cc_start: 0.3274 (mtm) cc_final: 0.2354 (pmm) REVERT: 1 1422 THR cc_start: 0.6717 (p) cc_final: 0.6507 (t) REVERT: 1 1482 ASP cc_start: 0.0005 (OUTLIER) cc_final: -0.0408 (m-30) REVERT: 1 1507 GLN cc_start: 0.1865 (OUTLIER) cc_final: 0.1263 (pt0) REVERT: L 179 SER cc_start: 0.2221 (OUTLIER) cc_final: 0.1983 (t) REVERT: H 34 SER cc_start: -0.2758 (OUTLIER) cc_final: -0.3013 (m) REVERT: H 166 THR cc_start: 0.5885 (t) cc_final: 0.5421 (p) outliers start: 43 outliers final: 3 residues processed: 200 average time/residue: 1.0116 time to fit residues: 229.3025 Evaluate side-chains 85 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 351 THR Chi-restraints excluded: chain 1 residue 1482 ASP Chi-restraints excluded: chain 1 residue 1507 GLN Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 61 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 108 GLN ** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 551 ASN ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11034 GLN A ** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11208 ASN ** 11418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11507 GLN 11510 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.155040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.116315 restraints weight = 85353.645| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 4.67 r_work: 0.3467 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0597 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14296 Z= 0.200 Angle : 0.775 12.247 19494 Z= 0.394 Chirality : 0.046 0.212 2131 Planarity : 0.006 0.059 2557 Dihedral : 5.993 46.021 1931 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 5.30 % Allowed : 26.90 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.21 (0.20), residues: 1784 helix: -0.52 (0.31), residues: 251 sheet: -1.55 (0.26), residues: 343 loop : -0.58 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 1 407 HIS 0.008 0.002 HIS 1 509 PHE 0.021 0.002 PHE 11421 TYR 0.026 0.002 TYR 1 728 ARG 0.009 0.001 ARG 11386 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 415) hydrogen bonds : angle 7.86173 ( 1126) SS BOND : bond 0.00755 ( 4) SS BOND : angle 1.61351 ( 8) covalent geometry : bond 0.00442 (14292) covalent geometry : angle 0.77399 (19486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 102 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 307 LYS cc_start: 0.3751 (tttm) cc_final: 0.3256 (mmmt) REVERT: 1 1087 SER cc_start: 0.0193 (OUTLIER) cc_final: -0.0476 (p) REVERT: 1 1338 GLN cc_start: 0.2358 (mp10) cc_final: 0.1938 (mp10) REVERT: 1 1427 ASP cc_start: -0.1921 (OUTLIER) cc_final: -0.2523 (t70) REVERT: 1 1456 VAL cc_start: -0.2418 (OUTLIER) cc_final: -0.2829 (p) REVERT: 1 1482 ASP cc_start: 0.0159 (OUTLIER) cc_final: -0.0138 (p0) REVERT: L 12 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.4389 (mp) REVERT: L 50 ILE cc_start: 0.2961 (OUTLIER) cc_final: 0.2674 (tp) REVERT: L 69 SER cc_start: 0.5020 (OUTLIER) cc_final: 0.4772 (t) REVERT: L 107 GLU cc_start: 0.5041 (pm20) cc_final: 0.4386 (pm20) REVERT: L 108 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5583 (mm) REVERT: H 37 LYS cc_start: 0.4498 (mptt) cc_final: 0.3555 (tmtt) REVERT: H 166 THR cc_start: 0.6446 (t) cc_final: 0.6034 (p) outliers start: 74 outliers final: 21 residues processed: 165 average time/residue: 0.8064 time to fit residues: 154.7512 Evaluate side-chains 108 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 351 THR Chi-restraints excluded: chain 1 residue 356 TRP Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 657 TYR Chi-restraints excluded: chain 1 residue 775 THR Chi-restraints excluded: chain 1 residue 859 VAL Chi-restraints excluded: chain 1 residue 1037 LEU Chi-restraints excluded: chain 1 residue 1087 SER Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1427 ASP Chi-restraints excluded: chain 1 residue 1436 VAL Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain 1 residue 1482 ASP Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 256 GLN ** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 428 GLN 1 551 ASN ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 964 ASN ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS H 0 GLN H 29 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.168140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.132858 restraints weight = 79999.948| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 4.72 r_work: 0.3705 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1328 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14296 Z= 0.293 Angle : 0.968 13.866 19494 Z= 0.499 Chirality : 0.054 0.272 2131 Planarity : 0.008 0.081 2557 Dihedral : 7.030 57.589 1923 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 39.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.68 % Rotamer: Outliers : 6.28 % Allowed : 24.74 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1784 helix: -1.23 (0.30), residues: 265 sheet: -1.46 (0.26), residues: 340 loop : -0.99 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP 1 898 HIS 0.012 0.003 HIS 11031 PHE 0.041 0.004 PHE 1 504 TYR 0.021 0.003 TYR 11057 ARG 0.016 0.002 ARG 11386 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 415) hydrogen bonds : angle 8.32661 ( 1126) SS BOND : bond 0.00708 ( 4) SS BOND : angle 1.60458 ( 8) covalent geometry : bond 0.00652 (14292) covalent geometry : angle 0.96794 (19486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 127 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 222 GLN cc_start: -0.0829 (OUTLIER) cc_final: -0.1508 (tp40) REVERT: 1 307 LYS cc_start: 0.4969 (tttm) cc_final: 0.4199 (mmmt) REVERT: 1 369 TRP cc_start: 0.3897 (m100) cc_final: 0.2584 (m100) REVERT: 1 501 LEU cc_start: 0.0123 (tp) cc_final: -0.0143 (tp) REVERT: 1 653 HIS cc_start: 0.2763 (m170) cc_final: 0.2205 (m90) REVERT: 1 1473 ARG cc_start: 0.3403 (OUTLIER) cc_final: 0.1819 (ttt180) REVERT: 1 1502 LEU cc_start: 0.2852 (mt) cc_final: 0.2015 (mt) REVERT: L 40 GLN cc_start: 0.3337 (pp30) cc_final: 0.2725 (mp10) REVERT: L 41 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.4531 (mmt-90) REVERT: L 49 LEU cc_start: 0.1875 (OUTLIER) cc_final: 0.1363 (mp) REVERT: L 79 ARG cc_start: 0.7229 (pmt170) cc_final: 0.6898 (pmm-80) REVERT: L 207 ILE cc_start: 0.7047 (mp) cc_final: 0.6539 (tt) REVERT: L 215 GLU cc_start: 0.3659 (mm-30) cc_final: 0.3365 (mm-30) REVERT: H 63 THR cc_start: 0.1851 (OUTLIER) cc_final: 0.1483 (m) REVERT: H 77 LEU cc_start: 0.4572 (OUTLIER) cc_final: 0.3871 (tm) outliers start: 89 outliers final: 22 residues processed: 205 average time/residue: 0.9272 time to fit residues: 216.3628 Evaluate side-chains 133 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 222 GLN Chi-restraints excluded: chain 1 residue 427 LEU Chi-restraints excluded: chain 1 residue 549 MET Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 657 TYR Chi-restraints excluded: chain 1 residue 943 SER Chi-restraints excluded: chain 1 residue 953 ASP Chi-restraints excluded: chain 1 residue 966 THR Chi-restraints excluded: chain 1 residue 1027 TYR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1402 THR Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain 1 residue 1473 ARG Chi-restraints excluded: chain L residue -1 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 148 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 168 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 980 ASN 11208 ASN ** 11373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** H 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.167093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.130123 restraints weight = 84043.778| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 4.81 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1107 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14296 Z= 0.176 Angle : 0.756 11.136 19494 Z= 0.382 Chirality : 0.047 0.213 2131 Planarity : 0.006 0.068 2557 Dihedral : 6.040 24.879 1920 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 4.12 % Allowed : 26.77 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.50 (0.19), residues: 1784 helix: -0.88 (0.31), residues: 254 sheet: -1.38 (0.26), residues: 342 loop : -0.88 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 1 810 HIS 0.013 0.002 HIS 1 393 PHE 0.037 0.002 PHE L 57 TYR 0.018 0.002 TYR 11042 ARG 0.010 0.001 ARG 1 697 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 415) hydrogen bonds : angle 7.70137 ( 1126) SS BOND : bond 0.00574 ( 4) SS BOND : angle 1.16849 ( 8) covalent geometry : bond 0.00402 (14292) covalent geometry : angle 0.75533 (19486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 307 LYS cc_start: 0.4931 (tttm) cc_final: 0.4194 (mmmt) REVERT: 1 1495 ASN cc_start: 0.3585 (p0) cc_final: 0.3271 (p0) REVERT: L 12 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3829 (tp) REVERT: L 35 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4720 (tt) REVERT: L 40 GLN cc_start: 0.3160 (pp30) cc_final: 0.2863 (mp10) REVERT: L 133 SER cc_start: 0.5216 (OUTLIER) cc_final: 0.4469 (t) REVERT: L 186 ASP cc_start: 0.7894 (p0) cc_final: 0.7673 (p0) REVERT: L 207 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6634 (tt) REVERT: L 215 GLU cc_start: 0.3729 (mm-30) cc_final: 0.3428 (mm-30) outliers start: 56 outliers final: 22 residues processed: 148 average time/residue: 0.8630 time to fit residues: 147.8445 Evaluate side-chains 118 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 372 SER Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 427 LEU Chi-restraints excluded: chain 1 residue 533 THR Chi-restraints excluded: chain 1 residue 1083 GLN Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 207 ILE Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 967 ASN ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11023 GLN 11265 ASN ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.170557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134112 restraints weight = 92155.171| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 5.10 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1266 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14296 Z= 0.187 Angle : 0.779 10.867 19494 Z= 0.394 Chirality : 0.047 0.211 2131 Planarity : 0.006 0.067 2557 Dihedral : 6.102 26.440 1920 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 3.80 % Allowed : 27.75 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.59 (0.19), residues: 1784 helix: -0.86 (0.31), residues: 259 sheet: -1.43 (0.25), residues: 365 loop : -0.95 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 898 HIS 0.009 0.002 HIS 1 393 PHE 0.032 0.002 PHE 11476 TYR 0.018 0.002 TYR 1 728 ARG 0.013 0.001 ARG 1 65 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 415) hydrogen bonds : angle 7.57544 ( 1126) SS BOND : bond 0.00668 ( 4) SS BOND : angle 0.98675 ( 8) covalent geometry : bond 0.00427 (14292) covalent geometry : angle 0.77859 (19486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 81 LEU cc_start: 0.1877 (OUTLIER) cc_final: 0.1614 (tp) REVERT: 1 217 LEU cc_start: -0.0001 (OUTLIER) cc_final: -0.0304 (tp) REVERT: 1 307 LYS cc_start: 0.5154 (tttm) cc_final: 0.4402 (mmmt) REVERT: 1 369 TRP cc_start: 0.3708 (m100) cc_final: 0.2474 (m100) REVERT: 1 374 LEU cc_start: 0.1308 (OUTLIER) cc_final: 0.0805 (pp) REVERT: 1 385 ARG cc_start: -0.1218 (OUTLIER) cc_final: -0.2372 (pmm150) REVERT: 1 549 MET cc_start: -0.0585 (OUTLIER) cc_final: -0.1807 (pmt) REVERT: 1 714 THR cc_start: 0.4052 (p) cc_final: 0.3833 (m) REVERT: 1 768 GLN cc_start: 0.1129 (OUTLIER) cc_final: -0.1179 (mt0) REVERT: L 12 LEU cc_start: 0.4192 (OUTLIER) cc_final: 0.3847 (tp) REVERT: L 40 GLN cc_start: 0.3292 (pp30) cc_final: 0.3056 (mp10) REVERT: L 57 PHE cc_start: 0.2045 (OUTLIER) cc_final: 0.1221 (m-80) REVERT: L 207 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6639 (tt) REVERT: L 215 GLU cc_start: 0.3686 (mm-30) cc_final: 0.3405 (mm-30) outliers start: 51 outliers final: 25 residues processed: 143 average time/residue: 0.9105 time to fit residues: 150.2216 Evaluate side-chains 128 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 385 ARG Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 427 LEU Chi-restraints excluded: chain 1 residue 549 MET Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 712 LYS Chi-restraints excluded: chain 1 residue 768 GLN Chi-restraints excluded: chain 1 residue 1010 ARG Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1134 TYR Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1402 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 57 PHE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 207 ILE Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 469 GLN ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN H 0 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.172988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.136380 restraints weight = 106047.626| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 5.56 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1262 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14296 Z= 0.168 Angle : 0.746 9.928 19494 Z= 0.376 Chirality : 0.046 0.170 2131 Planarity : 0.006 0.051 2557 Dihedral : 5.908 26.273 1920 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 3.86 % Allowed : 27.95 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1784 helix: -0.72 (0.31), residues: 254 sheet: -1.47 (0.25), residues: 378 loop : -0.89 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 1 709 HIS 0.007 0.001 HIS 1 393 PHE 0.030 0.002 PHE 11476 TYR 0.019 0.002 TYR 1 728 ARG 0.010 0.001 ARG 1 93 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 415) hydrogen bonds : angle 7.34801 ( 1126) SS BOND : bond 0.00676 ( 4) SS BOND : angle 0.86355 ( 8) covalent geometry : bond 0.00383 (14292) covalent geometry : angle 0.74630 (19486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 81 LEU cc_start: 0.1904 (OUTLIER) cc_final: 0.1632 (tp) REVERT: 1 217 LEU cc_start: -0.0126 (OUTLIER) cc_final: -0.0469 (tp) REVERT: 1 222 GLN cc_start: -0.1684 (OUTLIER) cc_final: -0.1915 (mm-40) REVERT: 1 307 LYS cc_start: 0.5201 (tttm) cc_final: 0.4345 (mmmt) REVERT: 1 369 TRP cc_start: 0.3624 (m100) cc_final: 0.2448 (m100) REVERT: L 12 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.3535 (tp) REVERT: L 36 GLU cc_start: 0.7157 (mp0) cc_final: 0.6467 (pm20) REVERT: L 207 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6684 (tt) REVERT: L 215 GLU cc_start: 0.3645 (mm-30) cc_final: 0.3347 (mm-30) REVERT: H 12 MET cc_start: 0.4564 (pmm) cc_final: 0.4063 (pmm) REVERT: H 28 MET cc_start: 0.1788 (pmm) cc_final: 0.1055 (tmm) REVERT: H 75 MET cc_start: 0.2663 (OUTLIER) cc_final: 0.0688 (tpp) REVERT: H 101 MET cc_start: 0.3817 (OUTLIER) cc_final: 0.3614 (mpt) REVERT: H 136 MET cc_start: 0.6211 (ppp) cc_final: 0.5574 (tpp) REVERT: H 175 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6693 (tm) outliers start: 51 outliers final: 25 residues processed: 141 average time/residue: 0.8942 time to fit residues: 144.5689 Evaluate side-chains 126 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 222 GLN Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 438 HIS Chi-restraints excluded: chain 1 residue 458 VAL Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 943 SER Chi-restraints excluded: chain 1 residue 1010 ARG Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1134 TYR Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain 1 residue 1459 LYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 207 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 256 GLN ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11208 ASN ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11481 GLN 11510 GLN H 33 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.177918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.142570 restraints weight = 99556.026| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 5.56 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1547 moved from start: 0.7466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 14296 Z= 0.210 Angle : 0.829 10.308 19494 Z= 0.422 Chirality : 0.049 0.250 2131 Planarity : 0.006 0.055 2557 Dihedral : 6.247 28.492 1920 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 32.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.11 % Favored : 92.77 % Rotamer: Outliers : 3.93 % Allowed : 27.95 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1784 helix: -1.18 (0.29), residues: 276 sheet: -1.33 (0.25), residues: 379 loop : -1.14 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP 11183 HIS 0.016 0.002 HIS H 165 PHE 0.041 0.003 PHE 11498 TYR 0.034 0.003 TYR L 38 ARG 0.010 0.001 ARG 1 436 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 415) hydrogen bonds : angle 7.50771 ( 1126) SS BOND : bond 0.00618 ( 4) SS BOND : angle 0.69476 ( 8) covalent geometry : bond 0.00489 (14292) covalent geometry : angle 0.82907 (19486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.1492 (mmp80) cc_final: 0.1254 (tpp80) REVERT: 1 217 LEU cc_start: -0.0183 (OUTLIER) cc_final: -0.0550 (tp) REVERT: 1 307 LYS cc_start: 0.5471 (tttm) cc_final: 0.4632 (mmmt) REVERT: 1 385 ARG cc_start: -0.1143 (OUTLIER) cc_final: -0.2011 (pmm150) REVERT: 1 768 GLN cc_start: 0.2143 (OUTLIER) cc_final: -0.1736 (mt0) REVERT: 1 1027 TYR cc_start: 0.1720 (OUTLIER) cc_final: 0.1414 (t80) REVERT: 1 1116 GLN cc_start: 0.3664 (tp40) cc_final: 0.3223 (OUTLIER) REVERT: 1 1377 MET cc_start: 0.1458 (mtm) cc_final: 0.1156 (mtm) REVERT: 1 1423 HIS cc_start: 0.1892 (p90) cc_final: 0.0957 (p90) REVERT: 1 1440 TYR cc_start: 0.3147 (m-80) cc_final: 0.2856 (m-80) REVERT: 1 1455 MET cc_start: -0.1349 (pp-130) cc_final: -0.2492 (tpt) REVERT: 1 1468 GLN cc_start: 0.1671 (tp-100) cc_final: 0.1392 (pm20) REVERT: L 12 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3589 (tp) REVERT: L 36 GLU cc_start: 0.7455 (mp0) cc_final: 0.7121 (mp0) REVERT: L 57 PHE cc_start: 0.2062 (OUTLIER) cc_final: 0.1356 (m-80) REVERT: L 207 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6692 (tt) REVERT: H 75 MET cc_start: 0.2442 (ppp) cc_final: 0.0749 (tpt) REVERT: H 136 MET cc_start: 0.6201 (ppp) cc_final: 0.5673 (tpp) REVERT: H 175 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6731 (tm) REVERT: H 214 ARG cc_start: -0.0293 (OUTLIER) cc_final: -0.1741 (ptp90) outliers start: 52 outliers final: 26 residues processed: 157 average time/residue: 0.8794 time to fit residues: 159.2888 Evaluate side-chains 139 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 385 ARG Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 438 HIS Chi-restraints excluded: chain 1 residue 458 VAL Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 768 GLN Chi-restraints excluded: chain 1 residue 943 SER Chi-restraints excluded: chain 1 residue 1027 TYR Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1134 TYR Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 57 PHE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 207 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 214 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 0.0000 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 190 GLN ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11083 GLN ** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 139 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.179408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.144074 restraints weight = 105194.114| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 5.67 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1471 moved from start: 0.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14296 Z= 0.181 Angle : 0.795 9.618 19494 Z= 0.400 Chirality : 0.047 0.229 2131 Planarity : 0.006 0.053 2557 Dihedral : 6.101 27.640 1920 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 3.73 % Allowed : 28.93 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.79 (0.19), residues: 1784 helix: -1.06 (0.30), residues: 266 sheet: -1.48 (0.25), residues: 383 loop : -1.10 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 1 369 HIS 0.010 0.002 HIS H 165 PHE 0.030 0.003 PHE 11498 TYR 0.020 0.002 TYR 1 728 ARG 0.010 0.001 ARG 11473 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 415) hydrogen bonds : angle 7.38933 ( 1126) SS BOND : bond 0.00573 ( 4) SS BOND : angle 0.71036 ( 8) covalent geometry : bond 0.00421 (14292) covalent geometry : angle 0.79521 (19486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 307 LYS cc_start: 0.5547 (tttm) cc_final: 0.4686 (mmmt) REVERT: 1 385 ARG cc_start: -0.1297 (OUTLIER) cc_final: -0.2143 (mpp80) REVERT: 1 768 GLN cc_start: 0.2161 (OUTLIER) cc_final: -0.1936 (mt0) REVERT: 1 1116 GLN cc_start: 0.3626 (tp40) cc_final: 0.3130 (mm110) REVERT: 1 1377 MET cc_start: 0.1480 (mtm) cc_final: 0.1197 (mtm) REVERT: 1 1455 MET cc_start: -0.1071 (pp-130) cc_final: -0.2283 (tpt) REVERT: L 12 LEU cc_start: 0.3820 (OUTLIER) cc_final: 0.3420 (tp) REVERT: L 36 GLU cc_start: 0.7298 (mp0) cc_final: 0.7024 (mp0) REVERT: L 39 LEU cc_start: 0.5716 (tt) cc_final: 0.5242 (pt) REVERT: L 57 PHE cc_start: 0.2138 (OUTLIER) cc_final: 0.1407 (m-80) REVERT: H 75 MET cc_start: 0.2441 (ppp) cc_final: 0.0744 (tpp) REVERT: H 136 MET cc_start: 0.6152 (ppp) cc_final: 0.5671 (tpp) REVERT: H 214 ARG cc_start: -0.0312 (OUTLIER) cc_final: -0.1725 (ptp90) outliers start: 49 outliers final: 28 residues processed: 152 average time/residue: 0.8942 time to fit residues: 155.4788 Evaluate side-chains 142 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 385 ARG Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 438 HIS Chi-restraints excluded: chain 1 residue 458 VAL Chi-restraints excluded: chain 1 residue 653 HIS Chi-restraints excluded: chain 1 residue 768 GLN Chi-restraints excluded: chain 1 residue 943 SER Chi-restraints excluded: chain 1 residue 1027 TYR Chi-restraints excluded: chain 1 residue 1054 VAL Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1134 TYR Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain 1 residue 1499 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 57 PHE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 214 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 967 ASN ** 11083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11241 HIS ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.181951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.147548 restraints weight = 107252.573| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 5.81 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4104 r_free = 0.4104 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1698 moved from start: 0.8695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14296 Z= 0.215 Angle : 0.871 10.443 19494 Z= 0.442 Chirality : 0.050 0.244 2131 Planarity : 0.007 0.069 2557 Dihedral : 6.461 29.061 1920 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 33.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.09 % Rotamer: Outliers : 3.34 % Allowed : 29.52 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.95 (0.19), residues: 1784 helix: -1.26 (0.29), residues: 277 sheet: -1.42 (0.25), residues: 374 loop : -1.26 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP 11183 HIS 0.010 0.002 HIS 1 393 PHE 0.035 0.003 PHE 11498 TYR 0.024 0.003 TYR 1 131 ARG 0.009 0.001 ARG 11473 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 415) hydrogen bonds : angle 7.67002 ( 1126) SS BOND : bond 0.01232 ( 4) SS BOND : angle 0.73746 ( 8) covalent geometry : bond 0.00501 (14292) covalent geometry : angle 0.87127 (19486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 307 LYS cc_start: 0.5751 (tttm) cc_final: 0.4942 (mmmt) REVERT: 1 385 ARG cc_start: -0.0828 (OUTLIER) cc_final: -0.1523 (pmm150) REVERT: 1 653 HIS cc_start: 0.2334 (OUTLIER) cc_final: 0.1763 (m90) REVERT: 1 768 GLN cc_start: 0.2806 (OUTLIER) cc_final: -0.1835 (mt0) REVERT: 1 943 SER cc_start: 0.2879 (OUTLIER) cc_final: 0.2649 (t) REVERT: 1 1377 MET cc_start: 0.1762 (mtm) cc_final: 0.1470 (mtm) REVERT: 1 1455 MET cc_start: -0.0872 (pp-130) cc_final: -0.2199 (tpt) REVERT: 1 1495 ASN cc_start: 0.4224 (p0) cc_final: 0.3991 (p0) REVERT: L 12 LEU cc_start: 0.4551 (OUTLIER) cc_final: 0.4063 (tp) REVERT: L 39 LEU cc_start: 0.6345 (tt) cc_final: 0.5893 (tm) REVERT: L 47 LYS cc_start: 0.6184 (mmtp) cc_final: 0.5809 (mmtp) REVERT: L 94 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8346 (p) REVERT: H 38 SER cc_start: 0.3988 (OUTLIER) cc_final: 0.3253 (t) REVERT: H 67 ASP cc_start: 0.5234 (t0) cc_final: 0.4714 (t0) REVERT: H 75 MET cc_start: 0.2204 (ppp) cc_final: 0.0552 (tpp) REVERT: H 136 MET cc_start: 0.6136 (ppp) cc_final: 0.5630 (tpp) REVERT: H 214 ARG cc_start: -0.0120 (OUTLIER) cc_final: -0.1579 (ptp90) outliers start: 43 outliers final: 26 residues processed: 153 average time/residue: 0.8900 time to fit residues: 156.3518 Evaluate side-chains 138 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 385 ARG Chi-restraints excluded: chain 1 residue 399 MET Chi-restraints excluded: chain 1 residue 419 ASP Chi-restraints excluded: chain 1 residue 458 VAL Chi-restraints excluded: chain 1 residue 653 HIS Chi-restraints excluded: chain 1 residue 768 GLN Chi-restraints excluded: chain 1 residue 901 ASP Chi-restraints excluded: chain 1 residue 943 SER Chi-restraints excluded: chain 1 residue 1010 ARG Chi-restraints excluded: chain 1 residue 1027 TYR Chi-restraints excluded: chain 1 residue 1054 VAL Chi-restraints excluded: chain 1 residue 1099 THR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1134 TYR Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain 1 residue 1499 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 214 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 139 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 156 optimal weight: 0.0370 chunk 146 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 515 HIS ** 1 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11105 ASN ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 212 ASN L 214 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.180192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.145811 restraints weight = 111278.452| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 5.88 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14296 Z= 0.165 Angle : 0.809 9.901 19494 Z= 0.406 Chirality : 0.048 0.255 2131 Planarity : 0.006 0.094 2557 Dihedral : 6.000 27.064 1920 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 2.55 % Allowed : 31.22 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % 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: -1.72 (0.20), residues: 1784 helix: -0.88 (0.30), residues: 280 sheet: -1.33 (0.26), residues: 378 loop : -1.13 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 150 HIS 0.005 0.001 HIS 1 653 PHE 0.029 0.002 PHE H 58 TYR 0.021 0.002 TYR H 74 ARG 0.013 0.001 ARG L 213 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 415) hydrogen bonds : angle 7.24789 ( 1126) SS BOND : bond 0.00748 ( 4) SS BOND : angle 0.91677 ( 8) covalent geometry : bond 0.00386 (14292) covalent geometry : angle 0.80920 (19486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.335 Fit side-chains REVERT: 1 307 LYS cc_start: 0.5629 (tttm) cc_final: 0.4864 (mmmt) REVERT: 1 385 ARG cc_start: -0.1148 (OUTLIER) cc_final: -0.1673 (pmm150) REVERT: 1 768 GLN cc_start: 0.2643 (OUTLIER) cc_final: -0.1753 (mt0) REVERT: 1 1377 MET cc_start: 0.1637 (mtm) cc_final: 0.1426 (mtm) REVERT: 1 1455 MET cc_start: -0.0797 (pp-130) cc_final: -0.2155 (tpt) REVERT: L 1 MET cc_start: 0.5024 (ttp) cc_final: 0.4548 (mmm) REVERT: L 8 LEU cc_start: 0.6173 (mt) cc_final: 0.5283 (pt) REVERT: L 12 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.3916 (tp) REVERT: L 47 LYS cc_start: 0.6143 (mmtp) cc_final: 0.5914 (mmtp) REVERT: H 28 MET cc_start: 0.3164 (ppp) cc_final: 0.2448 (pmm) REVERT: H 38 SER cc_start: 0.4696 (OUTLIER) cc_final: 0.4250 (t) REVERT: H 67 ASP cc_start: 0.5053 (t0) cc_final: 0.4569 (t0) REVERT: H 75 MET cc_start: 0.1982 (ppp) cc_final: 0.0678 (tpp) REVERT: H 136 MET cc_start: 0.6108 (ppp) cc_final: 0.5721 (tpp) REVERT: H 174 ASP cc_start: 0.8647 (m-30) cc_final: 0.7296 (t0) REVERT: H 214 ARG cc_start: -0.0209 (OUTLIER) cc_final: -0.1603 (ptp90) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.9564 time to fit residues: 140.8060 Evaluate side-chains 121 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 GLN Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 385 ARG Chi-restraints excluded: chain 1 residue 399 MET Chi-restraints excluded: chain 1 residue 458 VAL Chi-restraints excluded: chain 1 residue 510 VAL Chi-restraints excluded: chain 1 residue 768 GLN Chi-restraints excluded: chain 1 residue 1010 ARG Chi-restraints excluded: chain 1 residue 1027 TYR Chi-restraints excluded: chain 1 residue 1109 SER Chi-restraints excluded: chain 1 residue 1113 VAL Chi-restraints excluded: chain 1 residue 1339 LEU Chi-restraints excluded: chain 1 residue 1387 THR Chi-restraints excluded: chain 1 residue 1452 ASN Chi-restraints excluded: chain 1 residue 1456 VAL Chi-restraints excluded: chain 1 residue 1499 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 214 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 126 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 493 ASN ** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN H 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.189755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.155312 restraints weight = 106218.759| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 6.06 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1730 moved from start: 0.9422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14296 Z= 0.209 Angle : 0.870 10.878 19494 Z= 0.442 Chirality : 0.049 0.242 2131 Planarity : 0.007 0.072 2557 Dihedral : 6.366 30.482 1920 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.37 % Rotamer: Outliers : 2.62 % Allowed : 31.22 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.89 (0.19), residues: 1784 helix: -1.17 (0.28), residues: 286 sheet: -1.37 (0.26), residues: 369 loop : -1.24 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP 1 369 HIS 0.009 0.002 HIS 1 393 PHE 0.036 0.003 PHE L 211 TYR 0.024 0.002 TYR L 88 ARG 0.014 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 415) hydrogen bonds : angle 7.49880 ( 1126) SS BOND : bond 0.00832 ( 4) SS BOND : angle 0.97525 ( 8) covalent geometry : bond 0.00491 (14292) covalent geometry : angle 0.87005 (19486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10325.23 seconds wall clock time: 179 minutes 40.52 seconds (10780.52 seconds total)