Starting phenix.real_space_refine on Wed Feb 12 21:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.map" model { file = "/net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asa_11891/02_2025/7asa_11891.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 116 5.49 5 S 18 5.16 5 C 4646 2.51 5 N 1459 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8104 Number of models: 1 Model: "" Number of chains: 5 Chain: "0" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3993 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "2" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 730 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 8, 'rna3p': 25} Chain breaks: 1 Chain: "A" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1755 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 43, 'rna3p_pyr': 32} Link IDs: {'rna2p': 7, 'rna3p': 74} Chain breaks: 5 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 967 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Time building chain proxies: 6.50, per 1000 atoms: 0.80 Number of scatterers: 8104 At special positions: 0 Unit cell: (126.28, 146.78, 89.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 116 15.00 O 1865 8.00 N 1459 7.00 C 4646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.11 Conformation dependent library (CDL) restraints added in 731.9 milliseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 43.9% alpha, 18.0% beta 26 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain '0' and resid 4 through 20 removed outlier: 3.593A pdb=" N ASN 0 16 " --> pdb=" O THR 0 12 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS 0 18 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET 0 20 " --> pdb=" O ASN 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 83 removed outlier: 3.790A pdb=" N LEU 0 78 " --> pdb=" O MET 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 127 Processing helix chain '0' and resid 147 through 151 Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 192 through 200 Processing helix chain '0' and resid 204 through 214 Processing helix chain '0' and resid 223 through 236 Processing helix chain '0' and resid 269 through 279 Processing helix chain '0' and resid 280 through 317 removed outlier: 3.543A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS 0 314 " --> pdb=" O LYS 0 310 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 336 removed outlier: 3.610A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 414 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.679A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 0 423 " --> pdb=" O ILE 0 419 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU 0 425 " --> pdb=" O GLU 0 421 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 0 426 " --> pdb=" O ILE 0 422 " (cutoff:3.500A) Processing helix chain '0' and resid 466 through 475 Processing helix chain '0' and resid 503 through 516 removed outlier: 4.462A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE 0 513 " --> pdb=" O GLU 0 509 " (cutoff:3.500A) Processing helix chain '0' and resid 561 through 565 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 25 Processing helix chain '1' and resid 68 through 75 removed outlier: 4.141A pdb=" N ALA 1 73 " --> pdb=" O LYS 1 69 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN 1 74 " --> pdb=" O GLU 1 70 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 32 removed outlier: 4.670A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.529A pdb=" N ALA K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.484A pdb=" N LYS K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 114 through 116 No H-bonds generated for 'chain 'K' and resid 114 through 116' Processing helix chain 'K' and resid 120 through 134 Processing sheet with id=AA1, first strand: chain '0' and resid 23 through 31 removed outlier: 5.641A pdb=" N ILE 0 24 " --> pdb=" O ARG 0 40 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG 0 40 " --> pdb=" O ILE 0 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS 0 26 " --> pdb=" O HIS 0 38 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP 0 34 " --> pdb=" O PRO 0 30 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS 0 47 " --> pdb=" O THR 0 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 87 through 92 removed outlier: 6.607A pdb=" N HIS 0 103 " --> pdb=" O GLU 0 89 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE 0 91 " --> pdb=" O ILE 0 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE 0 101 " --> pdb=" O ILE 0 91 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP 0 141 " --> pdb=" O LEU 0 131 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP 0 133 " --> pdb=" O ILE 0 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE 0 139 " --> pdb=" O ASP 0 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 249 through 254 removed outlier: 3.790A pdb=" N LYS 0 249 " --> pdb=" O VAL 0 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AA5, first strand: chain '0' and resid 451 through 454 Processing sheet with id=AA6, first strand: chain '0' and resid 483 through 487 Processing sheet with id=AA7, first strand: chain '1' and resid 33 through 34 removed outlier: 6.858A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 14 Processing sheet with id=AA9, first strand: chain 'K' and resid 98 through 101 removed outlier: 6.453A pdb=" N ALA K 98 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU K 140 " --> pdb=" O ALA K 98 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL K 100 " --> pdb=" O GLU K 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 290 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1495 1.32 - 1.45: 2573 1.45 - 1.57: 4149 1.57 - 1.70: 224 1.70 - 1.82: 34 Bond restraints: 8475 Sorted by residual: bond pdb=" CA PRO 0 72 " pdb=" C PRO 0 72 " ideal model delta sigma weight residual 1.517 1.554 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" CZ ARG 0 286 " pdb=" NH2 ARG 0 286 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.30e-02 5.92e+03 1.57e+01 bond pdb=" N ARG 0 265 " pdb=" CA ARG 0 265 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" CZ ARG 0 116 " pdb=" NH2 ARG 0 116 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" CZ ARG 0 395 " pdb=" NH2 ARG 0 395 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 8470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 9394 2.35 - 4.70: 2316 4.70 - 7.04: 264 7.04 - 9.39: 24 9.39 - 11.74: 2 Bond angle restraints: 12000 Sorted by residual: angle pdb=" O3' A 2 44 " pdb=" C3' A 2 44 " pdb=" C2' A 2 44 " ideal model delta sigma weight residual 109.50 121.24 -11.74 1.50e+00 4.44e-01 6.12e+01 angle pdb=" C4' C A2504 " pdb=" C3' C A2504 " pdb=" C2' C A2504 " ideal model delta sigma weight residual 102.60 96.30 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" CA ASN 0 335 " pdb=" CB ASN 0 335 " pdb=" CG ASN 0 335 " ideal model delta sigma weight residual 112.60 106.43 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" C3' U A2502 " pdb=" C2' U A2502 " pdb=" C1' U A2502 " ideal model delta sigma weight residual 101.30 107.27 -5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" O3' C 2 13 " pdb=" C3' C 2 13 " pdb=" C2' C 2 13 " ideal model delta sigma weight residual 113.70 122.53 -8.83 1.50e+00 4.44e-01 3.46e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 4970 33.33 - 66.66: 284 66.66 - 99.98: 52 99.98 - 133.31: 2 133.31 - 166.64: 4 Dihedral angle restraints: 5312 sinusoidal: 3128 harmonic: 2184 Sorted by residual: dihedral pdb=" C5' U A1952 " pdb=" C4' U A1952 " pdb=" C3' U A1952 " pdb=" O3' U A1952 " ideal model delta sinusoidal sigma weight residual 147.00 73.30 73.70 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" O4' U A1952 " pdb=" C4' U A1952 " pdb=" C3' U A1952 " pdb=" C2' U A1952 " ideal model delta sinusoidal sigma weight residual 24.00 -38.58 62.58 1 8.00e+00 1.56e-02 8.09e+01 dihedral pdb=" O4' U 2 34 " pdb=" C1' U 2 34 " pdb=" N1 U 2 34 " pdb=" C2 U 2 34 " ideal model delta sinusoidal sigma weight residual 200.00 53.28 146.72 1 1.50e+01 4.44e-03 7.83e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1212 0.133 - 0.266: 225 0.266 - 0.399: 19 0.399 - 0.533: 3 0.533 - 0.666: 1 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CA ASN 0 335 " pdb=" N ASN 0 335 " pdb=" C ASN 0 335 " pdb=" CB ASN 0 335 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASN 0 151 " pdb=" N ASN 0 151 " pdb=" C ASN 0 151 " pdb=" CB ASN 0 151 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA ASN K 93 " pdb=" N ASN K 93 " pdb=" C ASN K 93 " pdb=" CB ASN K 93 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 1457 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1113 " -0.286 2.00e-02 2.50e+03 1.17e-01 3.73e+02 pdb=" N9 A A1113 " 0.075 2.00e-02 2.50e+03 pdb=" C8 A A1113 " 0.105 2.00e-02 2.50e+03 pdb=" N7 A A1113 " 0.056 2.00e-02 2.50e+03 pdb=" C5 A A1113 " 0.037 2.00e-02 2.50e+03 pdb=" C6 A A1113 " -0.052 2.00e-02 2.50e+03 pdb=" N6 A A1113 " -0.150 2.00e-02 2.50e+03 pdb=" N1 A A1113 " -0.025 2.00e-02 2.50e+03 pdb=" C2 A A1113 " 0.048 2.00e-02 2.50e+03 pdb=" N3 A A1113 " 0.102 2.00e-02 2.50e+03 pdb=" C4 A A1113 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2692 " -0.256 2.00e-02 2.50e+03 1.08e-01 3.52e+02 pdb=" N9 G A2692 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G A2692 " 0.066 2.00e-02 2.50e+03 pdb=" N7 G A2692 " 0.039 2.00e-02 2.50e+03 pdb=" C5 G A2692 " 0.053 2.00e-02 2.50e+03 pdb=" C6 G A2692 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G A2692 " -0.161 2.00e-02 2.50e+03 pdb=" N1 G A2692 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A2692 " 0.071 2.00e-02 2.50e+03 pdb=" N2 G A2692 " -0.072 2.00e-02 2.50e+03 pdb=" N3 G A2692 " 0.119 2.00e-02 2.50e+03 pdb=" C4 G A2692 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1097 " -0.277 2.00e-02 2.50e+03 1.13e-01 3.52e+02 pdb=" N9 A A1097 " 0.073 2.00e-02 2.50e+03 pdb=" C8 A A1097 " 0.106 2.00e-02 2.50e+03 pdb=" N7 A A1097 " 0.050 2.00e-02 2.50e+03 pdb=" C5 A A1097 " 0.038 2.00e-02 2.50e+03 pdb=" C6 A A1097 " -0.033 2.00e-02 2.50e+03 pdb=" N6 A A1097 " -0.153 2.00e-02 2.50e+03 pdb=" N1 A A1097 " -0.029 2.00e-02 2.50e+03 pdb=" C2 A A1097 " 0.044 2.00e-02 2.50e+03 pdb=" N3 A A1097 " 0.096 2.00e-02 2.50e+03 pdb=" C4 A A1097 " 0.086 2.00e-02 2.50e+03 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3477 2.97 - 3.45: 8175 3.45 - 3.94: 14307 3.94 - 4.42: 15716 4.42 - 4.90: 22968 Nonbonded interactions: 64643 Sorted by model distance: nonbonded pdb=" O3' G 2 35 " pdb=" O2' G 2 35 " model vdw 2.490 2.432 nonbonded pdb=" O2' G A2688 " pdb=" OP1 A A2689 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP 0 34 " pdb=" OG SER 0 51 " model vdw 2.528 3.040 nonbonded pdb=" O3' G 2 39 " pdb=" O2' G 2 39 " model vdw 2.535 2.432 nonbonded pdb=" O THR K 131 " pdb=" OG SER K 134 " model vdw 2.544 3.040 ... (remaining 64638 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.580 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.013 0.063 8475 Z= 0.833 Angle : 1.976 11.739 12000 Z= 1.304 Chirality : 0.104 0.666 1460 Planarity : 0.022 0.117 1126 Dihedral : 20.131 166.638 3890 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.54 % Favored : 95.78 % Rotamer: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.26), residues: 734 helix: -1.59 (0.24), residues: 297 sheet: -0.45 (0.55), residues: 87 loop : -1.66 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.019 0.004 HIS 0 33 PHE 0.091 0.016 PHE 0 207 TYR 0.130 0.025 TYR 0 31 ARG 0.012 0.002 ARG 1 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8098 (t80) cc_final: 0.7539 (t80) REVERT: 0 102 PHE cc_start: 0.8000 (m-80) cc_final: 0.7430 (m-80) REVERT: 0 301 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7952 (mm-30) REVERT: 1 2 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8365 (mtp85) REVERT: 1 5 LYS cc_start: 0.8768 (tptt) cc_final: 0.7893 (tptt) REVERT: 1 8 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8638 (tptt) REVERT: 1 21 GLU cc_start: 0.7808 (tp30) cc_final: 0.7557 (tp30) REVERT: K 11 LEU cc_start: 0.9139 (mt) cc_final: 0.8825 (tt) REVERT: K 38 PHE cc_start: 0.6946 (t80) cc_final: 0.6675 (t80) REVERT: K 96 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8193 (mmtt) REVERT: K 129 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7747 (mt-10) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2662 time to fit residues: 77.6275 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 103 HIS 0 195 GLN 0 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.117278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104429 restraints weight = 25978.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107196 restraints weight = 13706.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108703 restraints weight = 6693.052| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8475 Z= 0.202 Angle : 0.731 11.761 12000 Z= 0.387 Chirality : 0.045 0.252 1460 Planarity : 0.004 0.037 1126 Dihedral : 21.559 179.479 2581 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.18 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 734 helix: 0.40 (0.29), residues: 299 sheet: -0.28 (0.46), residues: 126 loop : -1.10 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 259 PHE 0.014 0.002 PHE K 38 TYR 0.015 0.002 TYR 0 153 ARG 0.004 0.001 ARG 0 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8023 (t80) cc_final: 0.7616 (t80) REVERT: 0 123 MET cc_start: 0.7851 (mtm) cc_final: 0.7400 (mmm) REVERT: 0 171 ILE cc_start: 0.6039 (mp) cc_final: 0.5807 (tp) REVERT: 0 283 GLU cc_start: 0.8471 (mp0) cc_final: 0.8160 (pm20) REVERT: 1 8 LYS cc_start: 0.9311 (tmtt) cc_final: 0.8652 (tptt) REVERT: 1 21 GLU cc_start: 0.7680 (tp30) cc_final: 0.7420 (tp30) REVERT: 1 64 LYS cc_start: 0.8253 (mmmt) cc_final: 0.8003 (mmmm) REVERT: K 57 GLU cc_start: 0.7620 (tp30) cc_final: 0.6818 (tp30) REVERT: K 72 THR cc_start: 0.9030 (m) cc_final: 0.8731 (t) REVERT: K 91 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7033 (mt-10) outliers start: 14 outliers final: 10 residues processed: 176 average time/residue: 0.2368 time to fit residues: 54.3892 Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 67 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 0.0470 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 HIS 0 33 HIS 0 145 HIS 0 300 ASN 0 326 GLN 1 31 ASN K 12 GLN K 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.114933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.101893 restraints weight = 26081.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104897 restraints weight = 13459.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106054 restraints weight = 6183.758| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8475 Z= 0.263 Angle : 0.716 8.491 12000 Z= 0.375 Chirality : 0.045 0.248 1460 Planarity : 0.005 0.034 1126 Dihedral : 21.649 178.540 2581 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 5.13 % Allowed : 18.50 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 734 helix: 0.45 (0.29), residues: 305 sheet: -0.42 (0.43), residues: 139 loop : -1.29 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.013 0.002 HIS 0 60 PHE 0.013 0.002 PHE 0 207 TYR 0.016 0.002 TYR 0 278 ARG 0.005 0.001 ARG 1 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7986 (mtm) cc_final: 0.7688 (mmm) REVERT: 0 171 ILE cc_start: 0.6125 (mp) cc_final: 0.5886 (tp) REVERT: 0 278 TYR cc_start: 0.8681 (m-10) cc_final: 0.8382 (m-80) REVERT: 0 421 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: 1 8 LYS cc_start: 0.9266 (tmtt) cc_final: 0.8698 (tptp) REVERT: 1 14 LYS cc_start: 0.8664 (mptt) cc_final: 0.8269 (mmtp) REVERT: 1 21 GLU cc_start: 0.7648 (tp30) cc_final: 0.7334 (tp30) REVERT: K 72 THR cc_start: 0.9016 (m) cc_final: 0.8763 (t) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.2216 time to fit residues: 46.8055 Evaluate side-chains 144 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 54 optimal weight: 0.6980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103250 restraints weight = 25869.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106146 restraints weight = 13295.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107427 restraints weight = 6521.627| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8475 Z= 0.201 Angle : 0.650 7.766 12000 Z= 0.340 Chirality : 0.042 0.239 1460 Planarity : 0.004 0.036 1126 Dihedral : 21.648 178.184 2581 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 5.49 % Allowed : 20.33 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.31), residues: 734 helix: 0.69 (0.30), residues: 305 sheet: -0.34 (0.44), residues: 140 loop : -1.21 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.011 0.002 HIS 0 60 PHE 0.011 0.001 PHE 0 207 TYR 0.012 0.001 TYR 0 9 ARG 0.004 0.001 ARG 1 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 68 ASN cc_start: 0.6173 (OUTLIER) cc_final: 0.5933 (t0) REVERT: 0 123 MET cc_start: 0.7861 (mtm) cc_final: 0.7570 (mmm) REVERT: 0 171 ILE cc_start: 0.6188 (mp) cc_final: 0.5935 (tp) REVERT: 0 278 TYR cc_start: 0.8599 (m-80) cc_final: 0.8289 (m-80) REVERT: 0 283 GLU cc_start: 0.8492 (mp0) cc_final: 0.8261 (pm20) REVERT: 0 395 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7508 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8640 (tptt) REVERT: 1 21 GLU cc_start: 0.7545 (tp30) cc_final: 0.7273 (tp30) REVERT: 1 70 GLU cc_start: 0.8345 (pm20) cc_final: 0.7875 (pm20) REVERT: K 11 LEU cc_start: 0.8761 (tp) cc_final: 0.8547 (tt) REVERT: K 72 THR cc_start: 0.8927 (m) cc_final: 0.8688 (t) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.2244 time to fit residues: 47.1960 Evaluate side-chains 150 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 68 ASN Chi-restraints excluded: chain 0 residue 83 ILE Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 309 ILE Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.117889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105184 restraints weight = 25380.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108042 restraints weight = 12983.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.109425 restraints weight = 6171.821| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8475 Z= 0.158 Angle : 0.611 9.626 12000 Z= 0.317 Chirality : 0.040 0.229 1460 Planarity : 0.004 0.061 1126 Dihedral : 21.491 177.668 2581 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 5.31 % Allowed : 21.06 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 734 helix: 1.06 (0.30), residues: 304 sheet: -0.17 (0.45), residues: 141 loop : -1.09 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.009 0.001 HIS 0 60 PHE 0.008 0.001 PHE 1 51 TYR 0.010 0.001 TYR 0 31 ARG 0.005 0.001 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5737 (mp) REVERT: 0 278 TYR cc_start: 0.8555 (m-80) cc_final: 0.8279 (m-80) REVERT: 0 382 LYS cc_start: 0.8513 (tppt) cc_final: 0.8283 (tppt) REVERT: 0 395 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7478 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9269 (tmtt) cc_final: 0.8722 (tptp) REVERT: 1 25 GLN cc_start: 0.8152 (mt0) cc_final: 0.7873 (mt0) REVERT: 1 70 GLU cc_start: 0.8000 (pm20) cc_final: 0.7601 (pm20) REVERT: K 57 GLU cc_start: 0.7552 (tp30) cc_final: 0.7231 (tp30) REVERT: K 72 THR cc_start: 0.8842 (m) cc_final: 0.8606 (t) outliers start: 29 outliers final: 19 residues processed: 161 average time/residue: 0.2181 time to fit residues: 46.4245 Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 68 ASN 1 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.116535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103657 restraints weight = 25762.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106540 restraints weight = 13449.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107909 restraints weight = 6277.146| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8475 Z= 0.208 Angle : 0.637 9.679 12000 Z= 0.328 Chirality : 0.041 0.233 1460 Planarity : 0.005 0.050 1126 Dihedral : 21.568 178.104 2581 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 6.04 % Allowed : 21.43 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.31), residues: 734 helix: 0.96 (0.30), residues: 304 sheet: -0.23 (0.45), residues: 137 loop : -1.02 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 60 PHE 0.009 0.001 PHE 0 267 TYR 0.008 0.001 TYR 0 162 ARG 0.004 0.001 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5619 (mp) REVERT: 0 278 TYR cc_start: 0.8517 (m-80) cc_final: 0.8239 (m-80) REVERT: 0 382 LYS cc_start: 0.8561 (tppt) cc_final: 0.8318 (tppt) REVERT: 0 395 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7475 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9301 (tmtt) cc_final: 0.8698 (tptt) REVERT: 1 21 GLU cc_start: 0.7604 (tp30) cc_final: 0.7368 (tp30) REVERT: 1 70 GLU cc_start: 0.8066 (pm20) cc_final: 0.7790 (pm20) REVERT: K 72 THR cc_start: 0.8900 (m) cc_final: 0.8676 (t) outliers start: 33 outliers final: 23 residues processed: 156 average time/residue: 0.2072 time to fit residues: 43.6782 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 67 THR Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103034 restraints weight = 25857.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105650 restraints weight = 13512.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106885 restraints weight = 6728.859| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8475 Z= 0.235 Angle : 0.671 10.583 12000 Z= 0.345 Chirality : 0.042 0.236 1460 Planarity : 0.005 0.061 1126 Dihedral : 21.669 178.521 2581 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 6.23 % Allowed : 21.43 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.31), residues: 734 helix: 0.77 (0.30), residues: 304 sheet: -0.33 (0.44), residues: 145 loop : -1.10 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.006 0.001 HIS 0 60 PHE 0.010 0.001 PHE 0 207 TYR 0.010 0.001 TYR 0 31 ARG 0.004 0.001 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7573 (mmm) cc_final: 0.7122 (mtp) REVERT: 0 240 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5577 (mp) REVERT: 0 278 TYR cc_start: 0.8496 (m-80) cc_final: 0.8216 (m-80) REVERT: 0 382 LYS cc_start: 0.8554 (tppt) cc_final: 0.8321 (tppt) REVERT: 0 395 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7516 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9308 (tmtt) cc_final: 0.8711 (tptt) REVERT: 1 21 GLU cc_start: 0.7597 (tp30) cc_final: 0.7320 (tp30) REVERT: 1 70 GLU cc_start: 0.8043 (pm20) cc_final: 0.7771 (pm20) outliers start: 34 outliers final: 25 residues processed: 160 average time/residue: 0.2088 time to fit residues: 44.6487 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.118335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105558 restraints weight = 25871.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108480 restraints weight = 12954.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109753 restraints weight = 6118.384| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8475 Z= 0.158 Angle : 0.621 11.029 12000 Z= 0.317 Chirality : 0.039 0.220 1460 Planarity : 0.004 0.059 1126 Dihedral : 21.480 177.647 2581 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 4.76 % Allowed : 22.53 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 734 helix: 0.88 (0.30), residues: 305 sheet: -0.09 (0.45), residues: 141 loop : -1.01 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.016 0.001 HIS 0 60 PHE 0.007 0.001 PHE 0 200 TYR 0.007 0.001 TYR 1 76 ARG 0.005 0.000 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7622 (mmm) cc_final: 0.7182 (mtp) REVERT: 0 240 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5703 (mp) REVERT: 0 278 TYR cc_start: 0.8475 (m-80) cc_final: 0.8187 (m-80) REVERT: 0 382 LYS cc_start: 0.8540 (tppt) cc_final: 0.8317 (tppt) REVERT: 0 395 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7421 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9279 (tmtt) cc_final: 0.8750 (tptp) REVERT: 1 21 GLU cc_start: 0.7594 (tp30) cc_final: 0.7268 (tp30) REVERT: 1 70 GLU cc_start: 0.8036 (pm20) cc_final: 0.7752 (pm20) outliers start: 26 outliers final: 21 residues processed: 152 average time/residue: 0.2267 time to fit residues: 45.5593 Evaluate side-chains 144 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 83 ILE Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 83 optimal weight: 0.6980 chunk 80 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.119066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106144 restraints weight = 26230.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.109102 restraints weight = 13160.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.110554 restraints weight = 6359.001| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8475 Z= 0.166 Angle : 0.636 10.720 12000 Z= 0.323 Chirality : 0.040 0.216 1460 Planarity : 0.005 0.068 1126 Dihedral : 21.438 177.472 2581 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 4.76 % Allowed : 23.26 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.32), residues: 734 helix: 0.96 (0.30), residues: 301 sheet: -0.17 (0.45), residues: 137 loop : -0.97 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 60 PHE 0.009 0.001 PHE 0 37 TYR 0.010 0.001 TYR 0 31 ARG 0.005 0.000 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 278 TYR cc_start: 0.8423 (m-80) cc_final: 0.8210 (m-80) REVERT: 0 395 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7342 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9280 (tmtt) cc_final: 0.8754 (tptp) REVERT: 1 21 GLU cc_start: 0.7643 (tp30) cc_final: 0.7230 (tp30) REVERT: K 106 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7604 (mtm-85) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.2247 time to fit residues: 42.7380 Evaluate side-chains 141 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.116769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103900 restraints weight = 25822.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106760 restraints weight = 13043.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107838 restraints weight = 6176.241| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8475 Z= 0.223 Angle : 0.677 9.241 12000 Z= 0.348 Chirality : 0.042 0.240 1460 Planarity : 0.005 0.065 1126 Dihedral : 21.549 177.885 2581 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 4.58 % Allowed : 23.99 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 734 helix: 0.87 (0.30), residues: 301 sheet: -0.15 (0.44), residues: 141 loop : -1.14 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.014 0.002 HIS 0 60 PHE 0.008 0.001 PHE 0 207 TYR 0.011 0.001 TYR 0 9 ARG 0.006 0.001 ARG K 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 272 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: 0 278 TYR cc_start: 0.8397 (m-80) cc_final: 0.8144 (m-80) REVERT: 0 283 GLU cc_start: 0.8405 (pm20) cc_final: 0.7985 (pm20) REVERT: 0 395 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7380 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9304 (tmtt) cc_final: 0.8712 (tptt) REVERT: 1 21 GLU cc_start: 0.7645 (tp30) cc_final: 0.7239 (tp30) REVERT: K 140 GLU cc_start: 0.5482 (pm20) cc_final: 0.4912 (pm20) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.2353 time to fit residues: 42.2008 Evaluate side-chains 140 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 272 GLU Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain 1 residue 83 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 151 ASN 1 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.101799 restraints weight = 26078.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104331 restraints weight = 13479.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.105723 restraints weight = 6528.817| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8475 Z= 0.288 Angle : 0.750 10.451 12000 Z= 0.383 Chirality : 0.045 0.244 1460 Planarity : 0.005 0.062 1126 Dihedral : 21.753 178.014 2581 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 5.49 % Allowed : 22.89 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.31), residues: 734 helix: 0.57 (0.29), residues: 307 sheet: -0.44 (0.44), residues: 140 loop : -1.35 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.013 0.002 HIS 0 60 PHE 0.011 0.002 PHE 0 377 TYR 0.013 0.002 TYR 0 251 ARG 0.005 0.001 ARG K 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.08 seconds wall clock time: 55 minutes 38.75 seconds (3338.75 seconds total)