Starting phenix.real_space_refine on Wed Feb 4 07:00:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivj_60928/02_2026/9ivj_60928.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5782 2.51 5 N 1505 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9053 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5053 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 628} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 764 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1428 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 810 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9053 At special positions: 0 Unit cell: (98.94, 122.91, 102.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1714 8.00 N 1505 7.00 C 5782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 138 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 216 " distance=2.02 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 101 " 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: 0.75 Conformation dependent library (CDL) restraints added in 403.0 milliseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 32.7% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.739A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.501A pdb=" N LEU A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 60 " --> pdb=" O TRP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.583A pdb=" N ILE A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.215A pdb=" N VAL A 107 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.658A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.636A pdb=" N LEU A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 231 through 242 removed outlier: 4.127A pdb=" N TYR A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 257 through 275 Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.895A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 Processing helix chain 'A' and resid 345 through 357 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 390 through 406 removed outlier: 4.180A pdb=" N GLY A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 removed outlier: 4.065A pdb=" N HIS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 removed outlier: 3.507A pdb=" N LEU A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.680A pdb=" N LYS A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.584A pdb=" N ASP B 57 " --> pdb=" O GLN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.007A pdb=" N SER B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.676A pdb=" N ALA C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.870A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.905A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 3.601A pdb=" N ARG B 78 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.741A pdb=" N LEU A 226 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 220 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 547 removed outlier: 3.783A pdb=" N VAL A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 582 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 577 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 605 removed outlier: 7.709A pdb=" N ILE A 602 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 673 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN A 604 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR A 658 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N GLY A 672 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 14.732A pdb=" N VAL A 656 " --> pdb=" O GLY A 672 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 619 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR A 631 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.585A pdb=" N PHE C 109 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 115 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.601A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.786A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR H 112 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N ASP H 102 " --> pdb=" O PRO H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.582A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.582A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 21 392 hydrogen bonds defined for protein. 1041 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: 1.55 Time building geometry restraints manager: 1.00 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: 2885 1.34 - 1.46: 2313 1.46 - 1.58: 3999 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 9272 Sorted by residual: bond pdb=" N ASN C 157 " pdb=" CA ASN C 157 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.53e+00 bond pdb=" C SER H 107 " pdb=" N VAL H 108 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.29e-02 6.01e+03 1.24e+00 bond pdb=" CB ASN C 126 " pdb=" CG ASN C 126 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB GLU B 121 " pdb=" CG GLU B 121 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CA ASN C 126 " pdb=" CB ASN C 126 " ideal model delta sigma weight residual 1.541 1.553 -0.012 1.20e-02 6.94e+03 9.90e-01 ... (remaining 9267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 12402 1.72 - 3.44: 179 3.44 - 5.17: 26 5.17 - 6.89: 8 6.89 - 8.61: 3 Bond angle restraints: 12618 Sorted by residual: angle pdb=" CA ARG B 105 " pdb=" CB ARG B 105 " pdb=" CG ARG B 105 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N ASN C 126 " pdb=" CA ASN C 126 " pdb=" C ASN C 126 " ideal model delta sigma weight residual 113.28 107.54 5.74 1.57e+00 4.06e-01 1.34e+01 angle pdb=" CA ASN C 126 " pdb=" CB ASN C 126 " pdb=" CG ASN C 126 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA GLN C 92 " pdb=" CB GLN C 92 " pdb=" CG GLN C 92 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" N VAL B 120 " pdb=" CA VAL B 120 " pdb=" C VAL B 120 " ideal model delta sigma weight residual 113.16 108.51 4.65 1.49e+00 4.50e-01 9.76e+00 ... (remaining 12613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4932 17.98 - 35.95: 456 35.95 - 53.93: 90 53.93 - 71.90: 10 71.90 - 89.88: 8 Dihedral angle restraints: 5496 sinusoidal: 2090 harmonic: 3406 Sorted by residual: dihedral pdb=" CB CYS C 102 " pdb=" SG CYS C 102 " pdb=" SG CYS C 115 " pdb=" CB CYS C 115 " ideal model delta sinusoidal sigma weight residual 93.00 169.16 -76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS C 99 " pdb=" SG CYS C 99 " pdb=" SG CYS C 138 " pdb=" CB CYS C 138 " ideal model delta sinusoidal sigma weight residual 93.00 136.91 -43.91 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS A 534 " pdb=" SG CYS A 534 " pdb=" SG CYS A 587 " pdb=" CB CYS A 587 " ideal model delta sinusoidal sigma weight residual -86.00 -121.88 35.88 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 5493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1157 0.046 - 0.093: 200 0.093 - 0.139: 78 0.139 - 0.185: 0 0.185 - 0.232: 1 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CB VAL B 31 " pdb=" CA VAL B 31 " pdb=" CG1 VAL B 31 " pdb=" CG2 VAL B 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA GLN C 92 " pdb=" N GLN C 92 " pdb=" C GLN C 92 " pdb=" CB GLN C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1433 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 126 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ASN C 126 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN C 126 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY C 127 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 560 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C VAL A 560 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 560 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 561 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO C 146 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.024 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 225 2.69 - 3.24: 9017 3.24 - 3.80: 14538 3.80 - 4.35: 18662 4.35 - 4.90: 31818 Nonbonded interactions: 74260 Sorted by model distance: nonbonded pdb=" O ASN C 126 " pdb=" ND2 ASN C 126 " model vdw 2.138 3.120 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 120 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR C 145 " pdb=" OD1 ASP C 147 " model vdw 2.169 3.040 nonbonded pdb=" O SER B 60 " pdb=" N GLY B 82 " model vdw 2.206 3.120 nonbonded pdb=" OG SER A 621 " pdb=" OG1 THR A 630 " model vdw 2.259 3.040 ... (remaining 74255 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9283 Z= 0.119 Angle : 0.551 8.609 12640 Z= 0.290 Chirality : 0.040 0.232 1436 Planarity : 0.004 0.043 1598 Dihedral : 13.985 89.879 3285 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.20 % Allowed : 19.13 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1161 helix: 2.23 (0.30), residues: 327 sheet: 0.06 (0.36), residues: 257 loop : -0.01 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 8 TYR 0.020 0.001 TYR H 115 PHE 0.011 0.001 PHE A 148 TRP 0.013 0.001 TRP H 83 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9272) covalent geometry : angle 0.54907 (12618) SS BOND : bond 0.00397 ( 11) SS BOND : angle 1.28270 ( 22) hydrogen bonds : bond 0.19898 ( 383) hydrogen bonds : angle 7.38632 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.364 Fit side-chains REVERT: A 26 HIS cc_start: 0.6631 (m-70) cc_final: 0.6034 (m90) REVERT: A 44 MET cc_start: 0.7080 (mmm) cc_final: 0.6831 (mmm) REVERT: A 100 MET cc_start: 0.6170 (mtp) cc_final: 0.5701 (tpp) REVERT: A 106 LYS cc_start: 0.6607 (mttt) cc_final: 0.6403 (mtpp) REVERT: A 141 THR cc_start: 0.7096 (m) cc_final: 0.6735 (p) REVERT: A 264 TYR cc_start: 0.6639 (t80) cc_final: 0.6319 (t80) REVERT: A 308 THR cc_start: 0.7605 (m) cc_final: 0.7322 (p) REVERT: A 385 LYS cc_start: 0.7097 (mtmm) cc_final: 0.6561 (mtpp) REVERT: A 471 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6302 (tp30) REVERT: A 595 GLU cc_start: 0.7099 (pm20) cc_final: 0.6706 (tt0) REVERT: A 636 SER cc_start: 0.8285 (t) cc_final: 0.8040 (p) REVERT: A 655 HIS cc_start: 0.5969 (m90) cc_final: 0.5720 (m170) REVERT: B 46 SER cc_start: 0.7544 (t) cc_final: 0.7315 (p) REVERT: C 101 TYR cc_start: 0.6883 (t80) cc_final: 0.5698 (t80) REVERT: C 112 LYS cc_start: 0.8114 (mttp) cc_final: 0.7604 (mmtt) REVERT: C 169 VAL cc_start: 0.7849 (p) cc_final: 0.7418 (t) REVERT: C 173 ASN cc_start: 0.6882 (m-40) cc_final: 0.6657 (m-40) REVERT: C 183 LYS cc_start: 0.7298 (mmtt) cc_final: 0.6982 (mmtm) REVERT: H 93 MET cc_start: 0.6926 (ttm) cc_final: 0.6629 (tpp) REVERT: L 69 SER cc_start: 0.7084 (t) cc_final: 0.6804 (m) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.1065 time to fit residues: 28.3118 Evaluate side-chains 145 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 150 GLN A 344 GLN C 205 HIS H 6 GLN H 27 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102597 restraints weight = 11400.379| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.52 r_work: 0.3015 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9283 Z= 0.226 Angle : 0.631 7.446 12640 Z= 0.328 Chirality : 0.045 0.183 1436 Planarity : 0.005 0.048 1598 Dihedral : 4.301 28.027 1271 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.12 % Allowed : 18.13 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1161 helix: 1.75 (0.29), residues: 327 sheet: 0.06 (0.36), residues: 238 loop : -0.32 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 8 TYR 0.024 0.002 TYR C 94 PHE 0.015 0.002 PHE A 513 TRP 0.013 0.001 TRP H 47 HIS 0.006 0.002 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9272) covalent geometry : angle 0.62322 (12618) SS BOND : bond 0.01117 ( 11) SS BOND : angle 2.42051 ( 22) hydrogen bonds : bond 0.05110 ( 383) hydrogen bonds : angle 5.29700 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7853 (m-70) cc_final: 0.7462 (m-70) REVERT: A 100 MET cc_start: 0.6931 (mtp) cc_final: 0.6446 (tpt) REVERT: A 106 LYS cc_start: 0.7866 (mttt) cc_final: 0.7648 (mtpp) REVERT: A 141 THR cc_start: 0.8167 (m) cc_final: 0.7920 (p) REVERT: A 264 TYR cc_start: 0.8501 (t80) cc_final: 0.8294 (t80) REVERT: A 308 THR cc_start: 0.8587 (m) cc_final: 0.8339 (p) REVERT: A 385 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7865 (mtpp) REVERT: A 471 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7097 (tp30) REVERT: A 636 SER cc_start: 0.9190 (t) cc_final: 0.8969 (p) REVERT: A 655 HIS cc_start: 0.7125 (m90) cc_final: 0.6809 (m170) REVERT: C 101 TYR cc_start: 0.8041 (t80) cc_final: 0.7111 (t80) REVERT: C 112 LYS cc_start: 0.8466 (mttp) cc_final: 0.8137 (mmtt) REVERT: C 134 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7685 (mm-30) REVERT: C 161 SER cc_start: 0.9049 (t) cc_final: 0.8619 (m) REVERT: C 169 VAL cc_start: 0.8705 (p) cc_final: 0.8366 (t) REVERT: C 183 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7663 (mmtm) REVERT: H 16 GLN cc_start: 0.8353 (mt0) cc_final: 0.8005 (mt0) REVERT: L 81 GLN cc_start: 0.8076 (mt0) cc_final: 0.7608 (mt0) outliers start: 31 outliers final: 23 residues processed: 168 average time/residue: 0.1047 time to fit residues: 24.4339 Evaluate side-chains 160 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105891 restraints weight = 11211.351| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.56 r_work: 0.3024 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9283 Z= 0.138 Angle : 0.561 8.111 12640 Z= 0.292 Chirality : 0.042 0.155 1436 Planarity : 0.004 0.049 1598 Dihedral : 4.249 26.796 1271 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.63 % Allowed : 18.43 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1161 helix: 1.75 (0.29), residues: 328 sheet: -0.05 (0.35), residues: 236 loop : -0.40 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 8 TYR 0.015 0.001 TYR H 80 PHE 0.010 0.001 PHE C 141 TRP 0.013 0.001 TRP A 40 HIS 0.004 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9272) covalent geometry : angle 0.55726 (12618) SS BOND : bond 0.00650 ( 11) SS BOND : angle 1.72259 ( 22) hydrogen bonds : bond 0.04443 ( 383) hydrogen bonds : angle 4.91703 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7913 (m-70) cc_final: 0.7475 (m-70) REVERT: A 100 MET cc_start: 0.6850 (mtp) cc_final: 0.6434 (tpt) REVERT: A 141 THR cc_start: 0.8129 (m) cc_final: 0.7887 (p) REVERT: A 264 TYR cc_start: 0.8387 (t80) cc_final: 0.8100 (t80) REVERT: A 308 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 385 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7797 (mtpp) REVERT: A 655 HIS cc_start: 0.7057 (m90) cc_final: 0.6687 (m170) REVERT: C 101 TYR cc_start: 0.7973 (t80) cc_final: 0.7032 (t80) REVERT: C 112 LYS cc_start: 0.8464 (mttp) cc_final: 0.8119 (mmtt) REVERT: C 134 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7670 (mm-30) REVERT: C 169 VAL cc_start: 0.8708 (p) cc_final: 0.8356 (t) REVERT: C 183 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7588 (mmtm) REVERT: H 16 GLN cc_start: 0.8350 (mt0) cc_final: 0.7909 (mt0) REVERT: L 81 GLN cc_start: 0.8006 (mt0) cc_final: 0.7746 (mt0) outliers start: 36 outliers final: 25 residues processed: 169 average time/residue: 0.0957 time to fit residues: 22.6796 Evaluate side-chains 167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.0060 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN L 6 GLN L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107886 restraints weight = 11234.950| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.46 r_work: 0.3038 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.115 Angle : 0.537 6.755 12640 Z= 0.278 Chirality : 0.041 0.143 1436 Planarity : 0.004 0.049 1598 Dihedral : 4.135 22.393 1271 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.13 % Allowed : 18.23 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1161 helix: 1.87 (0.30), residues: 326 sheet: -0.00 (0.35), residues: 234 loop : -0.40 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 8 TYR 0.015 0.001 TYR H 115 PHE 0.010 0.001 PHE C 141 TRP 0.009 0.001 TRP A 40 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9272) covalent geometry : angle 0.53281 (12618) SS BOND : bond 0.00453 ( 11) SS BOND : angle 1.69819 ( 22) hydrogen bonds : bond 0.03972 ( 383) hydrogen bonds : angle 4.71755 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7842 (m-70) cc_final: 0.7556 (m-70) REVERT: A 100 MET cc_start: 0.6812 (mtp) cc_final: 0.6491 (tpt) REVERT: A 141 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7895 (p) REVERT: A 160 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8603 (pp) REVERT: A 308 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 339 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 385 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7816 (mtpp) REVERT: A 471 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 60 SER cc_start: 0.8273 (m) cc_final: 0.7983 (p) REVERT: C 101 TYR cc_start: 0.7938 (t80) cc_final: 0.7040 (t80) REVERT: C 112 LYS cc_start: 0.8458 (mttp) cc_final: 0.8131 (mmtt) REVERT: C 121 LYS cc_start: 0.8326 (ptmt) cc_final: 0.7950 (pttp) REVERT: C 134 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7613 (mm-30) REVERT: C 169 VAL cc_start: 0.8727 (p) cc_final: 0.8374 (t) REVERT: H 16 GLN cc_start: 0.8401 (mt0) cc_final: 0.7911 (mt0) REVERT: L 81 GLN cc_start: 0.8025 (mt0) cc_final: 0.7755 (mt0) outliers start: 41 outliers final: 28 residues processed: 166 average time/residue: 0.0878 time to fit residues: 20.7495 Evaluate side-chains 171 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107293 restraints weight = 11244.530| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.44 r_work: 0.3065 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9283 Z= 0.130 Angle : 0.524 6.466 12640 Z= 0.273 Chirality : 0.041 0.149 1436 Planarity : 0.004 0.049 1598 Dihedral : 4.119 26.955 1271 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.63 % Allowed : 17.93 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1161 helix: 2.04 (0.30), residues: 314 sheet: 0.10 (0.36), residues: 221 loop : -0.42 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.014 0.001 TYR H 80 PHE 0.010 0.001 PHE C 141 TRP 0.014 0.001 TRP A 40 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9272) covalent geometry : angle 0.52034 (12618) SS BOND : bond 0.00529 ( 11) SS BOND : angle 1.56047 ( 22) hydrogen bonds : bond 0.03985 ( 383) hydrogen bonds : angle 4.62901 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7848 (m-70) cc_final: 0.7508 (m-70) REVERT: A 100 MET cc_start: 0.6774 (mtp) cc_final: 0.6470 (tpt) REVERT: A 141 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7874 (p) REVERT: A 179 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: A 308 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8270 (p) REVERT: A 339 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.7874 (p) REVERT: A 385 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7835 (mtpp) REVERT: B 60 SER cc_start: 0.8256 (m) cc_final: 0.8007 (p) REVERT: C 101 TYR cc_start: 0.7927 (t80) cc_final: 0.7064 (t80) REVERT: C 112 LYS cc_start: 0.8472 (mttp) cc_final: 0.8137 (mmtt) REVERT: C 121 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7910 (pttp) REVERT: C 134 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7669 (mm-30) REVERT: C 169 VAL cc_start: 0.8726 (p) cc_final: 0.8360 (t) REVERT: L 81 GLN cc_start: 0.8039 (mt0) cc_final: 0.7768 (mt0) outliers start: 46 outliers final: 37 residues processed: 164 average time/residue: 0.0940 time to fit residues: 22.0871 Evaluate side-chains 178 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107181 restraints weight = 11229.537| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.43 r_work: 0.3048 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9283 Z= 0.129 Angle : 0.524 8.184 12640 Z= 0.272 Chirality : 0.040 0.148 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.096 25.405 1271 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.83 % Allowed : 17.52 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1161 helix: 2.07 (0.30), residues: 313 sheet: 0.09 (0.36), residues: 222 loop : -0.42 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 8 TYR 0.013 0.001 TYR A 572 PHE 0.009 0.001 PHE C 141 TRP 0.010 0.001 TRP A 40 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9272) covalent geometry : angle 0.52038 (12618) SS BOND : bond 0.00546 ( 11) SS BOND : angle 1.50917 ( 22) hydrogen bonds : bond 0.03918 ( 383) hydrogen bonds : angle 4.58185 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7818 (m-70) cc_final: 0.7483 (m-70) REVERT: A 100 MET cc_start: 0.6785 (mtp) cc_final: 0.6536 (tpt) REVERT: A 141 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7880 (p) REVERT: A 179 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: A 308 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8278 (p) REVERT: A 339 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.7887 (p) REVERT: A 385 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7824 (mtpp) REVERT: B 60 SER cc_start: 0.8230 (m) cc_final: 0.7991 (p) REVERT: C 101 TYR cc_start: 0.7933 (t80) cc_final: 0.7102 (t80) REVERT: C 112 LYS cc_start: 0.8453 (mttp) cc_final: 0.8117 (mmtt) REVERT: C 134 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7673 (mm-30) REVERT: C 169 VAL cc_start: 0.8736 (p) cc_final: 0.8397 (t) REVERT: H 16 GLN cc_start: 0.8343 (mt0) cc_final: 0.7910 (mt0) REVERT: L 81 GLN cc_start: 0.8063 (mt0) cc_final: 0.7792 (mt0) outliers start: 48 outliers final: 39 residues processed: 167 average time/residue: 0.0889 time to fit residues: 21.1624 Evaluate side-chains 180 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106727 restraints weight = 11368.264| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.45 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9283 Z= 0.135 Angle : 0.520 6.325 12640 Z= 0.271 Chirality : 0.040 0.148 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.102 25.272 1271 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.93 % Allowed : 17.62 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1161 helix: 2.05 (0.30), residues: 313 sheet: 0.07 (0.36), residues: 222 loop : -0.42 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.013 0.001 TYR A 572 PHE 0.009 0.001 PHE C 141 TRP 0.009 0.001 TRP A 40 HIS 0.006 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9272) covalent geometry : angle 0.51648 (12618) SS BOND : bond 0.00603 ( 11) SS BOND : angle 1.48600 ( 22) hydrogen bonds : bond 0.03940 ( 383) hydrogen bonds : angle 4.54175 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7801 (m-70) cc_final: 0.7472 (m-70) REVERT: A 100 MET cc_start: 0.6829 (mtp) cc_final: 0.6600 (tpt) REVERT: A 141 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7885 (p) REVERT: A 179 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8250 (ttp) REVERT: A 308 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 339 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 385 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7840 (mtpp) REVERT: B 60 SER cc_start: 0.8192 (m) cc_final: 0.7957 (p) REVERT: C 99 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7378 (p) REVERT: C 101 TYR cc_start: 0.7930 (t80) cc_final: 0.7142 (t80) REVERT: C 112 LYS cc_start: 0.8441 (mttp) cc_final: 0.8111 (mmtt) REVERT: C 134 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7720 (mm-30) REVERT: C 169 VAL cc_start: 0.8742 (p) cc_final: 0.8398 (t) REVERT: H 16 GLN cc_start: 0.8347 (mt0) cc_final: 0.8031 (mt0) REVERT: L 81 GLN cc_start: 0.8075 (mt0) cc_final: 0.7804 (mt0) outliers start: 49 outliers final: 39 residues processed: 170 average time/residue: 0.0820 time to fit residues: 20.1579 Evaluate side-chains 181 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 0.0020 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108338 restraints weight = 11473.911| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.54 r_work: 0.3099 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.112 Angle : 0.519 10.896 12640 Z= 0.267 Chirality : 0.040 0.145 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.063 24.247 1271 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.43 % Allowed : 18.73 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1161 helix: 2.12 (0.30), residues: 313 sheet: 0.14 (0.36), residues: 219 loop : -0.39 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.013 0.001 TYR A 572 PHE 0.009 0.001 PHE C 141 TRP 0.009 0.001 TRP A 40 HIS 0.005 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9272) covalent geometry : angle 0.51699 (12618) SS BOND : bond 0.00458 ( 11) SS BOND : angle 1.23950 ( 22) hydrogen bonds : bond 0.03746 ( 383) hydrogen bonds : angle 4.47460 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.367 Fit side-chains REVERT: A 26 HIS cc_start: 0.7833 (m-70) cc_final: 0.7548 (m-70) REVERT: A 44 MET cc_start: 0.8037 (mmm) cc_final: 0.7788 (mmm) REVERT: A 100 MET cc_start: 0.6840 (mtp) cc_final: 0.6629 (tpt) REVERT: A 179 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8175 (ttp) REVERT: A 308 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8278 (p) REVERT: A 339 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 385 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7821 (mtpp) REVERT: A 471 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 60 SER cc_start: 0.8236 (m) cc_final: 0.7992 (p) REVERT: C 94 TYR cc_start: 0.7199 (m-80) cc_final: 0.6777 (m-80) REVERT: C 99 CYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7376 (p) REVERT: C 101 TYR cc_start: 0.7899 (t80) cc_final: 0.7181 (t80) REVERT: C 112 LYS cc_start: 0.8417 (mttp) cc_final: 0.8101 (mmtt) REVERT: C 134 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7679 (mm-30) REVERT: C 169 VAL cc_start: 0.8746 (p) cc_final: 0.8426 (t) REVERT: H 16 GLN cc_start: 0.8311 (mt0) cc_final: 0.7809 (mt0) REVERT: L 81 GLN cc_start: 0.8066 (mt0) cc_final: 0.7793 (mt0) outliers start: 44 outliers final: 37 residues processed: 164 average time/residue: 0.0969 time to fit residues: 22.4144 Evaluate side-chains 172 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 655 HIS H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104490 restraints weight = 11474.764| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.54 r_work: 0.3049 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9283 Z= 0.175 Angle : 0.566 10.835 12640 Z= 0.291 Chirality : 0.042 0.155 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.182 25.402 1271 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.33 % Allowed : 18.83 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1161 helix: 1.97 (0.30), residues: 312 sheet: -0.11 (0.36), residues: 230 loop : -0.39 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.014 0.001 TYR A 157 PHE 0.011 0.001 PHE A 513 TRP 0.022 0.001 TRP A 40 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9272) covalent geometry : angle 0.56215 (12618) SS BOND : bond 0.00756 ( 11) SS BOND : angle 1.65691 ( 22) hydrogen bonds : bond 0.04191 ( 383) hydrogen bonds : angle 4.54240 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7714 (m90) cc_final: 0.7352 (m170) REVERT: A 44 MET cc_start: 0.8072 (mmm) cc_final: 0.7838 (mmm) REVERT: A 100 MET cc_start: 0.6865 (mtp) cc_final: 0.6616 (tpt) REVERT: A 179 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8275 (ttp) REVERT: A 308 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8251 (p) REVERT: A 339 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 385 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7852 (mtpp) REVERT: B 60 SER cc_start: 0.8247 (m) cc_final: 0.7976 (p) REVERT: C 94 TYR cc_start: 0.7388 (m-80) cc_final: 0.6874 (m-80) REVERT: C 99 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7402 (p) REVERT: C 101 TYR cc_start: 0.7932 (t80) cc_final: 0.7172 (t80) REVERT: C 112 LYS cc_start: 0.8410 (mttp) cc_final: 0.8105 (mmtt) REVERT: C 134 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7800 (mm-30) REVERT: C 169 VAL cc_start: 0.8756 (p) cc_final: 0.8404 (t) REVERT: H 16 GLN cc_start: 0.8328 (mt0) cc_final: 0.8020 (mt0) REVERT: L 81 GLN cc_start: 0.8090 (mt0) cc_final: 0.7823 (mt0) outliers start: 43 outliers final: 38 residues processed: 159 average time/residue: 0.0836 time to fit residues: 19.0541 Evaluate side-chains 173 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106499 restraints weight = 11448.986| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.48 r_work: 0.3077 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9283 Z= 0.131 Angle : 0.548 11.250 12640 Z= 0.281 Chirality : 0.041 0.147 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.160 24.867 1271 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.53 % Allowed : 18.73 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1161 helix: 2.01 (0.30), residues: 313 sheet: 0.00 (0.36), residues: 226 loop : -0.31 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.014 0.001 TYR A 572 PHE 0.010 0.001 PHE A 605 TRP 0.019 0.001 TRP A 40 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9272) covalent geometry : angle 0.54473 (12618) SS BOND : bond 0.00545 ( 11) SS BOND : angle 1.42977 ( 22) hydrogen bonds : bond 0.03950 ( 383) hydrogen bonds : angle 4.50598 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7776 (m90) cc_final: 0.7304 (m90) REVERT: A 44 MET cc_start: 0.8082 (mmm) cc_final: 0.7838 (mmm) REVERT: A 100 MET cc_start: 0.6918 (mtp) cc_final: 0.6711 (tpt) REVERT: A 179 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: A 339 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.7969 (p) REVERT: A 385 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7885 (mtpp) REVERT: B 60 SER cc_start: 0.8250 (m) cc_final: 0.7963 (p) REVERT: C 94 TYR cc_start: 0.7382 (m-80) cc_final: 0.6915 (m-80) REVERT: C 99 CYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7373 (p) REVERT: C 101 TYR cc_start: 0.7892 (t80) cc_final: 0.7181 (t80) REVERT: C 112 LYS cc_start: 0.8401 (mttp) cc_final: 0.8101 (mmtt) REVERT: C 134 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7798 (mm-30) REVERT: C 169 VAL cc_start: 0.8762 (p) cc_final: 0.8432 (t) REVERT: H 16 GLN cc_start: 0.8365 (mt0) cc_final: 0.8067 (mt0) REVERT: L 81 GLN cc_start: 0.8115 (mt0) cc_final: 0.7858 (mt0) outliers start: 45 outliers final: 37 residues processed: 156 average time/residue: 0.0825 time to fit residues: 18.4058 Evaluate side-chains 167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103551 restraints weight = 11313.407| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.34 r_work: 0.3031 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9283 Z= 0.253 Angle : 0.630 11.137 12640 Z= 0.324 Chirality : 0.044 0.157 1436 Planarity : 0.004 0.050 1598 Dihedral : 4.417 26.768 1271 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.53 % Allowed : 18.53 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1161 helix: 1.64 (0.29), residues: 312 sheet: -0.27 (0.36), residues: 236 loop : -0.50 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.017 0.002 TYR A 157 PHE 0.015 0.002 PHE A 513 TRP 0.009 0.001 TRP A 40 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 9272) covalent geometry : angle 0.62483 (12618) SS BOND : bond 0.01032 ( 11) SS BOND : angle 1.98926 ( 22) hydrogen bonds : bond 0.04636 ( 383) hydrogen bonds : angle 4.68733 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.34 seconds wall clock time: 55 minutes 40.23 seconds (3340.23 seconds total)