Starting phenix.real_space_refine on Wed Mar 12 23:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7asa_11891/03_2025/7asa_11891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asa_11891/03_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_11891/03_2025/7asa_11891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2025/7asa_11891.map" model { file = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2025/7asa_11891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_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-5624/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: 6.24, per 1000 atoms: 0.77 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: 2.15 Conformation dependent library (CDL) restraints added in 730.7 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: 2.92 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: 2.77 Time building geometry restraints manager: 2.55 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.050 Set scattering table: 0.080 Process input model: 24.820 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- 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 : 0.677 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: 0.2653 time to fit residues: 77.7399 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 : 0.742 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.104428 restraints weight = 25978.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107194 restraints weight = 13705.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108545 restraints weight = 6691.015| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.761 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: 0.8020 (t80) cc_final: 0.7611 (t80) REVERT: 0 123 MET cc_start: 0.7843 (mtm) cc_final: 0.7394 (mmm) REVERT: 0 171 ILE cc_start: 0.6035 (mp) cc_final: 0.5804 (tp) REVERT: 0 283 GLU cc_start: 0.8481 (mp0) cc_final: 0.8166 (pm20) REVERT: 1 8 LYS cc_start: 0.9316 (tmtt) cc_final: 0.8650 (tptt) REVERT: 1 21 GLU cc_start: 0.7660 (tp30) cc_final: 0.7409 (tp30) REVERT: 1 64 LYS cc_start: 0.8253 (mmmt) cc_final: 0.8005 (mmmm) REVERT: K 57 GLU cc_start: 0.7614 (tp30) cc_final: 0.6811 (tp30) REVERT: K 72 THR cc_start: 0.9026 (m) cc_final: 0.8730 (t) REVERT: K 91 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7043 (mt-10) outliers start: 14 outliers final: 10 residues processed: 176 average time/residue: 0.2335 time to fit residues: 53.8759 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 : 0.655 ------------------------------------------------------------------------------- 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: 0.0980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 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: 0.5798 ------------------------------------------------------------------------------- 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 0 300 ASN 0 326 GLN 1 31 ASN K 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.117304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104288 restraints weight = 26165.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107408 restraints weight = 13530.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108434 restraints weight = 6139.186| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4042 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= 0.182 Angle : 0.654 9.379 12000 Z= 0.343 Chirality : 0.043 0.235 1460 Planarity : 0.004 0.035 1126 Dihedral : 21.438 178.358 2581 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 4.03 % Allowed : 17.58 % Favored : 78.39 % 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: -0.43 (0.30), residues: 734 helix: 0.62 (0.30), residues: 306 sheet: -0.32 (0.43), residues: 141 loop : -1.16 (0.35), 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 0.009 0.001 PHE 0 207 TYR 0.012 0.001 TYR 0 278 ARG 0.003 0.001 ARG K 102 *********************** 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 172 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6023 (mp) cc_final: 0.5808 (tp) REVERT: 0 278 TYR cc_start: 0.8665 (m-10) cc_final: 0.8332 (m-80) REVERT: 0 283 GLU cc_start: 0.8515 (mp0) cc_final: 0.8251 (pm20) REVERT: 1 8 LYS cc_start: 0.9254 (tmtt) cc_final: 0.8683 (tptp) REVERT: 1 14 LYS cc_start: 0.8586 (mptt) cc_final: 0.8171 (mmtp) REVERT: 1 21 GLU cc_start: 0.7538 (tp30) cc_final: 0.7234 (tp30) REVERT: 1 70 GLU cc_start: 0.8152 (pm20) cc_final: 0.7779 (pm20) REVERT: K 72 THR cc_start: 0.8939 (m) cc_final: 0.8669 (t) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.2353 time to fit residues: 49.9660 Evaluate side-chains 143 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 SER 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 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP 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 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 Chi-restraints excluded: chain K residue 89 SER 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 HIS K 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.116386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103488 restraints weight = 25938.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106493 restraints weight = 13634.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107473 restraints weight = 6380.054| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4521 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= 0.207 Angle : 0.647 7.615 12000 Z= 0.337 Chirality : 0.042 0.235 1460 Planarity : 0.004 0.038 1126 Dihedral : 21.574 178.093 2581 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 5.49 % Allowed : 20.15 % Favored : 74.36 % 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: -0.31 (0.31), residues: 734 helix: 0.80 (0.30), residues: 304 sheet: -0.22 (0.45), residues: 135 loop : -1.20 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.002 HIS 0 60 PHE 0.011 0.001 PHE 0 37 TYR 0.010 0.001 TYR 0 403 ARG 0.005 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 : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6149 (mp) cc_final: 0.5884 (tp) REVERT: 0 278 TYR cc_start: 0.8591 (m-10) cc_final: 0.8281 (m-80) REVERT: 0 283 GLU cc_start: 0.8526 (mp0) cc_final: 0.8320 (pm20) REVERT: 0 395 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7470 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9256 (tmtt) cc_final: 0.8656 (tptt) REVERT: 1 21 GLU cc_start: 0.7516 (tp30) cc_final: 0.7277 (tp30) REVERT: K 72 THR cc_start: 0.8909 (m) cc_final: 0.8676 (t) outliers start: 30 outliers final: 22 residues processed: 160 average time/residue: 0.2271 time to fit residues: 48.2710 Evaluate side-chains 149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 126 HIS 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 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 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN ** K 93 ASN ** 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 = 0.3916 r_free = 0.3916 target = 0.116889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104073 restraints weight = 25594.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107163 restraints weight = 13212.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108038 restraints weight = 6105.608| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4757 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= 0.196 Angle : 0.634 9.263 12000 Z= 0.330 Chirality : 0.042 0.234 1460 Planarity : 0.005 0.061 1126 Dihedral : 21.543 178.134 2581 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 5.68 % Allowed : 20.70 % 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: -0.12 (0.31), residues: 734 helix: 0.93 (0.30), residues: 304 sheet: -0.11 (0.46), residues: 132 loop : -1.08 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.002 HIS 0 60 PHE 0.010 0.001 PHE 0 207 TYR 0.011 0.001 TYR 0 9 ARG 0.005 0.001 ARG K 64 *********************** 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 163 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6196 (mp) cc_final: 0.5949 (tp) REVERT: 0 240 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5720 (mp) REVERT: 0 278 TYR cc_start: 0.8570 (m-80) cc_final: 0.8279 (m-80) REVERT: 0 382 LYS cc_start: 0.8511 (tppt) cc_final: 0.8284 (tppt) REVERT: 0 395 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7454 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9292 (tmtt) cc_final: 0.8690 (tptt) REVERT: 1 21 GLU cc_start: 0.7489 (tp30) cc_final: 0.7242 (tp30) REVERT: K 72 THR cc_start: 0.8873 (m) cc_final: 0.8654 (t) outliers start: 31 outliers final: 21 residues processed: 153 average time/residue: 0.2073 time to fit residues: 42.9392 Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 126 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 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 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 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: 0.6980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN ** K 93 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.114925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102066 restraints weight = 26022.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104658 restraints weight = 14222.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106158 restraints weight = 6850.555| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8475 Z= 0.282 Angle : 0.711 9.498 12000 Z= 0.367 Chirality : 0.044 0.244 1460 Planarity : 0.005 0.051 1126 Dihedral : 21.794 178.861 2581 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 6.59 % Allowed : 19.60 % Favored : 73.81 % 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: -0.40 (0.31), residues: 734 helix: 0.72 (0.30), residues: 304 sheet: -0.25 (0.45), residues: 140 loop : -1.26 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.002 HIS 0 60 PHE 0.012 0.002 PHE 0 207 TYR 0.013 0.002 TYR 0 403 ARG 0.004 0.001 ARG K 64 *********************** 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 169 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 48 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6910 (tp) REVERT: 0 100 MET cc_start: 0.7628 (ttm) cc_final: 0.7424 (ttm) REVERT: 0 171 ILE cc_start: 0.6135 (mp) cc_final: 0.5879 (tp) REVERT: 0 240 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5384 (mm) REVERT: 0 278 TYR cc_start: 0.8480 (m-80) cc_final: 0.8185 (m-80) REVERT: 0 283 GLU cc_start: 0.8522 (mp0) cc_final: 0.8315 (pm20) REVERT: 0 395 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7477 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8726 (tptt) REVERT: 1 21 GLU cc_start: 0.7577 (tp30) cc_final: 0.7367 (tp30) outliers start: 36 outliers final: 27 residues processed: 158 average time/residue: 0.2077 time to fit residues: 43.9949 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 48 LEU Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 126 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 169 ASP 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 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 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 57 THR Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL 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: 2.9990 chunk 33 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN ** K 93 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.116024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102968 restraints weight = 25844.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105828 restraints weight = 13730.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107192 restraints weight = 6514.336| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5114 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= 0.204 Angle : 0.657 10.852 12000 Z= 0.338 Chirality : 0.042 0.235 1460 Planarity : 0.005 0.065 1126 Dihedral : 21.657 178.254 2581 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 7.14 % Allowed : 20.51 % 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: -0.24 (0.31), residues: 734 helix: 0.79 (0.30), residues: 306 sheet: -0.01 (0.46), residues: 135 loop : -1.20 (0.36), 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 0.010 0.001 PHE 0 207 TYR 0.008 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 172 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6049 (mp) cc_final: 0.5845 (tp) REVERT: 0 240 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5537 (mp) REVERT: 0 278 TYR cc_start: 0.8513 (m-80) cc_final: 0.8199 (m-80) REVERT: 0 283 GLU cc_start: 0.8503 (mp0) cc_final: 0.8253 (pm20) REVERT: 0 395 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7435 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8692 (tptt) REVERT: 1 21 GLU cc_start: 0.7571 (tp30) cc_final: 0.7344 (tp30) outliers start: 39 outliers final: 28 residues processed: 158 average time/residue: 0.2044 time to fit residues: 43.6665 Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 126 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 169 ASP 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 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 79 LEU Chi-restraints excluded: chain K residue 24 VAL 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: 0.9980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 ASN ** K 93 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.117310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104277 restraints weight = 26069.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107030 restraints weight = 14050.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.108405 restraints weight = 6946.074| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5341 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= 0.180 Angle : 0.640 10.664 12000 Z= 0.329 Chirality : 0.041 0.227 1460 Planarity : 0.005 0.059 1126 Dihedral : 21.552 177.818 2581 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 5.86 % Allowed : 21.61 % 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: -0.19 (0.31), residues: 734 helix: 0.82 (0.29), residues: 307 sheet: -0.25 (0.45), residues: 137 loop : -1.02 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.016 0.002 HIS 0 60 PHE 0.008 0.001 PHE 0 207 TYR 0.008 0.001 TYR 0 162 ARG 0.005 0.001 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: 32 poor density : 131 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7357 (mmm) cc_final: 0.7093 (mmm) REVERT: 0 240 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5670 (mp) REVERT: 0 278 TYR cc_start: 0.8478 (m-80) cc_final: 0.8172 (m-80) REVERT: 1 8 LYS cc_start: 0.9303 (tmtt) cc_final: 0.8740 (tptp) REVERT: 1 21 GLU cc_start: 0.7601 (tp30) cc_final: 0.7349 (tp30) outliers start: 32 outliers final: 26 residues processed: 151 average time/residue: 0.2072 time to fit residues: 42.2443 Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 126 HIS Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 169 ASP 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 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 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 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: 0.0060 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 ASN K 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.105892 restraints weight = 26394.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108354 restraints weight = 13989.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110049 restraints weight = 7150.062| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5594 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= 0.160 Angle : 0.621 9.429 12000 Z= 0.318 Chirality : 0.040 0.217 1460 Planarity : 0.005 0.067 1126 Dihedral : 21.444 177.533 2581 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 4.76 % Allowed : 23.08 % Favored : 72.16 % 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: -0.02 (0.31), residues: 734 helix: 0.97 (0.30), residues: 301 sheet: 0.01 (0.45), residues: 141 loop : -1.01 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.005 0.001 HIS 0 60 PHE 0.009 0.001 PHE 0 279 TYR 0.010 0.001 TYR 0 31 ARG 0.009 0.001 ARG K 64 *********************** 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 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5734 (mp) REVERT: 0 278 TYR cc_start: 0.8442 (m-80) cc_final: 0.8141 (m-80) REVERT: 0 395 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7397 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9282 (tmtt) cc_final: 0.8747 (tptp) REVERT: 1 21 GLU cc_start: 0.7568 (tp30) cc_final: 0.7251 (tp30) REVERT: K 102 ARG cc_start: 0.6719 (mmm-85) cc_final: 0.6454 (tpp80) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.2151 time to fit residues: 41.5413 Evaluate side-chains 142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 126 HIS 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 299 VAL 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 30 ILE 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 134 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: 0.0010 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 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 = 0.3935 r_free = 0.3935 target = 0.118160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105241 restraints weight = 25617.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108023 restraints weight = 13309.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109441 restraints weight = 6302.345| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8475 Z= 0.180 Angle : 0.646 10.561 12000 Z= 0.332 Chirality : 0.041 0.220 1460 Planarity : 0.005 0.068 1126 Dihedral : 21.387 177.502 2581 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 5.31 % Allowed : 23.81 % Favored : 70.88 % 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: -0.01 (0.32), residues: 734 helix: 1.09 (0.30), residues: 298 sheet: -0.23 (0.44), residues: 142 loop : -0.98 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.005 0.001 HIS 0 60 PHE 0.007 0.001 PHE 0 207 TYR 0.007 0.001 TYR 0 9 ARG 0.009 0.001 ARG K 94 ********************** 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 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7146 (mmm) cc_final: 0.6897 (tpt) REVERT: 0 240 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5693 (mp) REVERT: 0 278 TYR cc_start: 0.8481 (m-80) cc_final: 0.8169 (m-80) REVERT: 0 395 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7453 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9293 (tmtt) cc_final: 0.8739 (tptp) REVERT: 1 21 GLU cc_start: 0.7717 (tp30) cc_final: 0.7304 (tp30) REVERT: K 77 VAL cc_start: 0.8881 (m) cc_final: 0.8598 (p) REVERT: K 140 GLU cc_start: 0.4254 (pp20) cc_final: 0.3712 (pm20) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 0.2034 time to fit residues: 38.6038 Evaluate side-chains 139 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 126 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 299 VAL 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 399 GLU 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 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 89 SER Chi-restraints excluded: chain K residue 134 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: 0.7980 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 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 = 0.3925 r_free = 0.3925 target = 0.117472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.104574 restraints weight = 25995.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107449 restraints weight = 13511.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108666 restraints weight = 6417.542| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8475 Z= 0.203 Angle : 0.664 8.821 12000 Z= 0.340 Chirality : 0.042 0.225 1460 Planarity : 0.005 0.066 1126 Dihedral : 21.457 177.648 2581 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 4.76 % Allowed : 24.91 % Favored : 70.33 % 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: -0.08 (0.31), residues: 734 helix: 0.92 (0.29), residues: 304 sheet: -0.06 (0.45), residues: 141 loop : -1.02 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.005 0.001 HIS 0 60 PHE 0.008 0.001 PHE 0 377 TYR 0.013 0.001 TYR 0 31 ARG 0.009 0.001 ARG K 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.25 seconds wall clock time: 61 minutes 31.86 seconds (3691.86 seconds total)