Starting phenix.real_space_refine on Sat Apr 6 11:22:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_11891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_11891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_11891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_11891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asa_11891/04_2024/7asa_11891.pdb" } 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 Residue "0 GLU 14": "OE1" <-> "OE2" Residue "0 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 133": "OD1" <-> "OD2" Residue "0 ASP 193": "OD1" <-> "OD2" Residue "0 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 256": "OE1" <-> "OE2" Residue "0 GLU 263": "OE1" <-> "OE2" Residue "0 ASP 275": "OD1" <-> "OD2" Residue "0 GLU 295": "OE1" <-> "OE2" Residue "0 GLU 317": "OE1" <-> "OE2" Residue "0 TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 347": "OE1" <-> "OE2" Residue "0 GLU 355": "OE1" <-> "OE2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.08, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.09 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: 4.02 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: 96.30 - 104.36: 457 104.36 - 112.41: 4165 112.41 - 120.46: 4308 120.46 - 128.52: 2914 128.52 - 136.57: 156 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 2.440 nonbonded pdb=" OD1 ASP 0 34 " pdb=" OG SER 0 51 " model vdw 2.528 2.440 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 2.440 ... (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 ========== 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: 5.460 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: 14.850 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.670 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 0.739 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: 0.2701 time to fit residues: 78.8185 Evaluate side-chains 145 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 0 300 ASN 0 398 GLN ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3305 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= 0.217 Angle : 0.734 11.584 12000 Z= 0.387 Chirality : 0.045 0.243 1460 Planarity : 0.004 0.036 1126 Dihedral : 21.602 179.518 2581 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.41 % Rotamer: Outliers : 3.11 % Allowed : 15.57 % Favored : 81.32 % 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: -0.67 (0.30), residues: 734 helix: 0.38 (0.29), residues: 299 sheet: -0.45 (0.43), residues: 141 loop : -1.20 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 259 PHE 0.015 0.002 PHE K 38 TYR 0.014 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 189 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8169 (t80) cc_final: 0.7608 (t80) REVERT: 0 123 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: 0 171 ILE cc_start: 0.5997 (mp) cc_final: 0.5727 (tp) REVERT: 0 283 GLU cc_start: 0.8463 (mp0) cc_final: 0.8211 (pm20) REVERT: 1 8 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8611 (tptt) REVERT: 1 21 GLU cc_start: 0.7765 (tp30) cc_final: 0.7476 (tp30) REVERT: 1 64 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8186 (mmmm) REVERT: 1 68 LYS cc_start: 0.8633 (mptt) cc_final: 0.8365 (mmtt) REVERT: 1 80 LYS cc_start: 0.8640 (ptpt) cc_final: 0.7956 (ptpt) REVERT: K 11 LEU cc_start: 0.9171 (mt) cc_final: 0.8948 (tp) REVERT: K 57 GLU cc_start: 0.7590 (tp30) cc_final: 0.7172 (tp30) REVERT: K 91 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6954 (mt-10) REVERT: K 102 ARG cc_start: 0.7123 (mmm-85) cc_final: 0.6626 (ttm110) outliers start: 17 outliers final: 11 residues processed: 179 average time/residue: 0.2297 time to fit residues: 53.2868 Evaluate side-chains 152 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 123 MET 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 0 residue 380 TYR Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 74 ASN 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 42 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 HIS ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 ASN K 12 GLN K 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8475 Z= 0.223 Angle : 0.683 9.510 12000 Z= 0.356 Chirality : 0.044 0.235 1460 Planarity : 0.004 0.032 1126 Dihedral : 21.559 179.023 2581 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 4.58 % Allowed : 18.50 % Favored : 76.92 % 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: -0.47 (0.30), residues: 734 helix: 0.65 (0.30), residues: 305 sheet: -0.37 (0.43), residues: 140 loop : -1.25 (0.35), residues: 289 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 0.002 PHE 0 207 TYR 0.011 0.002 TYR 0 31 ARG 0.003 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 fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8134 (t80) cc_final: 0.7877 (t80) REVERT: 0 123 MET cc_start: 0.8014 (mtm) cc_final: 0.7699 (mmm) REVERT: 0 171 ILE cc_start: 0.5643 (mp) cc_final: 0.5406 (tp) REVERT: 0 278 TYR cc_start: 0.8540 (m-10) cc_final: 0.8225 (m-80) REVERT: 1 8 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8603 (tptt) REVERT: 1 10 SER cc_start: 0.8872 (m) cc_final: 0.8558 (p) REVERT: 1 21 GLU cc_start: 0.7763 (tp30) cc_final: 0.7399 (tp30) REVERT: K 11 LEU cc_start: 0.9023 (mt) cc_final: 0.8784 (tp) REVERT: K 64 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6703 (mtp85) REVERT: K 72 THR cc_start: 0.9100 (m) cc_final: 0.8755 (t) REVERT: K 102 ARG cc_start: 0.6989 (mmm-85) cc_final: 0.6619 (tpp80) outliers start: 25 outliers final: 17 residues processed: 162 average time/residue: 0.2406 time to fit residues: 49.9753 Evaluate side-chains 148 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 327 LEU Chi-restraints excluded: chain 0 residue 380 TYR 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 1 residue 74 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.0770 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 326 GLN ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8475 Z= 0.167 Angle : 0.619 7.573 12000 Z= 0.320 Chirality : 0.041 0.221 1460 Planarity : 0.004 0.039 1126 Dihedral : 21.436 178.383 2581 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 4.76 % Allowed : 20.33 % Favored : 74.91 % 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: -0.25 (0.31), residues: 734 helix: 0.94 (0.30), residues: 306 sheet: -0.36 (0.43), residues: 141 loop : -1.22 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 60 PHE 0.008 0.001 PHE 0 207 TYR 0.011 0.001 TYR 0 153 ARG 0.003 0.000 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 175 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8122 (t80) cc_final: 0.7869 (t80) REVERT: 0 80 ARG cc_start: 0.5944 (mpp80) cc_final: 0.5325 (mpp80) REVERT: 0 123 MET cc_start: 0.7940 (mtm) cc_final: 0.7656 (mmm) REVERT: 0 171 ILE cc_start: 0.5934 (mp) cc_final: 0.5688 (tp) REVERT: 0 278 TYR cc_start: 0.8523 (m-10) cc_final: 0.8219 (m-80) REVERT: 0 283 GLU cc_start: 0.8409 (mp0) cc_final: 0.8188 (pm20) REVERT: 0 382 LYS cc_start: 0.8489 (tppt) cc_final: 0.8246 (tppt) REVERT: 0 395 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7476 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9316 (tmtt) cc_final: 0.8634 (tptp) REVERT: 1 10 SER cc_start: 0.8936 (m) cc_final: 0.8490 (p) REVERT: 1 68 LYS cc_start: 0.8256 (mptt) cc_final: 0.7947 (mmtm) REVERT: K 11 LEU cc_start: 0.8959 (mt) cc_final: 0.8711 (tp) REVERT: K 72 THR cc_start: 0.9003 (m) cc_final: 0.8658 (t) outliers start: 26 outliers final: 16 residues processed: 165 average time/residue: 0.2378 time to fit residues: 51.0434 Evaluate side-chains 150 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS 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 309 ILE Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG 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 36 MET Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 HIS 0 410 GLN K 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8475 Z= 0.385 Angle : 0.793 9.150 12000 Z= 0.409 Chirality : 0.047 0.245 1460 Planarity : 0.005 0.041 1126 Dihedral : 21.889 179.838 2581 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 6.96 % Allowed : 19.05 % Favored : 73.99 % 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: -0.81 (0.30), residues: 734 helix: 0.49 (0.29), residues: 307 sheet: -0.62 (0.43), residues: 145 loop : -1.57 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.002 HIS 0 60 PHE 0.017 0.002 PHE 0 207 TYR 0.014 0.002 TYR 0 403 ARG 0.006 0.001 ARG K 106 *********************** 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 178 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 84 GLU cc_start: 0.7524 (tt0) cc_final: 0.7101 (tp30) REVERT: 0 123 MET cc_start: 0.8025 (mtm) cc_final: 0.7712 (mmm) REVERT: 0 171 ILE cc_start: 0.6104 (mp) cc_final: 0.5865 (tp) REVERT: 0 240 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5282 (mm) REVERT: 0 278 TYR cc_start: 0.8530 (m-10) cc_final: 0.8211 (m-80) REVERT: 0 395 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7583 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9343 (tmtt) cc_final: 0.8644 (tptt) REVERT: K 11 LEU cc_start: 0.9020 (mt) cc_final: 0.8713 (tp) REVERT: K 72 THR cc_start: 0.9145 (m) cc_final: 0.8849 (t) REVERT: K 140 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.4778 (pm20) outliers start: 38 outliers final: 26 residues processed: 165 average time/residue: 0.2369 time to fit residues: 51.1970 Evaluate side-chains 163 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 74 MET 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 368 THR Chi-restraints excluded: chain 0 residue 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 406 GLN 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 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET 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 140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** 0 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4969 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= 0.201 Angle : 0.646 11.015 12000 Z= 0.334 Chirality : 0.041 0.227 1460 Planarity : 0.004 0.037 1126 Dihedral : 21.653 178.845 2581 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 5.86 % Allowed : 21.06 % Favored : 73.08 % 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: -0.45 (0.31), residues: 734 helix: 0.79 (0.30), residues: 307 sheet: -0.22 (0.45), residues: 135 loop : -1.48 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.011 0.001 HIS 0 60 PHE 0.010 0.001 PHE 0 207 TYR 0.011 0.001 TYR 0 380 ARG 0.004 0.000 ARG K 106 *********************** 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 178 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: 0 171 ILE cc_start: 0.5956 (mp) cc_final: 0.5744 (tp) REVERT: 0 240 ILE cc_start: 0.5793 (OUTLIER) cc_final: 0.5496 (mp) REVERT: 0 278 TYR cc_start: 0.8464 (m-10) cc_final: 0.8175 (m-80) REVERT: 0 395 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7522 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9340 (tmtt) cc_final: 0.8684 (tptp) REVERT: 1 17 THR cc_start: 0.8526 (m) cc_final: 0.8230 (p) REVERT: 1 25 GLN cc_start: 0.8286 (mt0) cc_final: 0.7736 (mt0) REVERT: K 11 LEU cc_start: 0.8951 (mt) cc_final: 0.8653 (tp) REVERT: K 72 THR cc_start: 0.9045 (m) cc_final: 0.8736 (t) REVERT: K 100 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7267 (t) REVERT: K 140 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4725 (pm20) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 0.2358 time to fit residues: 50.5941 Evaluate side-chains 165 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 83 ILE Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU 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 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 406 GLN 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 36 MET 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 100 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.0050 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.2006 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8475 Z= 0.264 Angle : 0.688 9.207 12000 Z= 0.356 Chirality : 0.043 0.232 1460 Planarity : 0.005 0.038 1126 Dihedral : 21.755 179.045 2581 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 5.86 % Allowed : 23.08 % Favored : 71.06 % 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: -0.55 (0.31), residues: 734 helix: 0.70 (0.30), residues: 307 sheet: -0.40 (0.44), residues: 140 loop : -1.47 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.004 0.001 HIS 0 60 PHE 0.012 0.002 PHE 0 207 TYR 0.011 0.002 TYR 0 380 ARG 0.004 0.000 ARG K 106 *********************** 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 169 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 84 GLU cc_start: 0.7469 (tt0) cc_final: 0.7176 (tp30) REVERT: 0 123 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: 0 171 ILE cc_start: 0.5982 (mp) cc_final: 0.5768 (tp) REVERT: 0 240 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5291 (mm) REVERT: 0 278 TYR cc_start: 0.8488 (m-10) cc_final: 0.8210 (m-80) REVERT: 0 283 GLU cc_start: 0.8412 (mp0) cc_final: 0.8210 (pm20) REVERT: 0 395 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7524 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8656 (tptp) REVERT: 1 17 THR cc_start: 0.8534 (m) cc_final: 0.8198 (p) REVERT: 1 68 LYS cc_start: 0.8265 (mptt) cc_final: 0.8051 (mmtt) REVERT: 1 70 GLU cc_start: 0.8368 (pm20) cc_final: 0.8167 (pm20) REVERT: K 11 LEU cc_start: 0.8954 (mt) cc_final: 0.8627 (tp) REVERT: K 72 THR cc_start: 0.9074 (m) cc_final: 0.8779 (t) REVERT: K 100 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7229 (t) REVERT: K 140 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4550 (pm20) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.2457 time to fit residues: 49.9478 Evaluate side-chains 164 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU 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 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET 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 100 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 126 HIS 1 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5343 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= 0.168 Angle : 0.613 9.432 12000 Z= 0.314 Chirality : 0.039 0.219 1460 Planarity : 0.004 0.043 1126 Dihedral : 21.511 178.091 2581 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 5.13 % Allowed : 23.26 % 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: -0.25 (0.31), residues: 734 helix: 0.95 (0.30), residues: 307 sheet: -0.17 (0.45), residues: 136 loop : -1.35 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.003 0.001 HIS 0 60 PHE 0.007 0.001 PHE 0 207 TYR 0.010 0.001 TYR 0 380 ARG 0.003 0.000 ARG K 106 *********************** 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 176 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5529 (mp) REVERT: 0 278 TYR cc_start: 0.8461 (m-10) cc_final: 0.8193 (m-80) REVERT: 0 382 LYS cc_start: 0.8634 (tppt) cc_final: 0.8368 (tppt) REVERT: 0 395 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7433 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9299 (tmtt) cc_final: 0.8667 (tptp) REVERT: 1 17 THR cc_start: 0.8440 (m) cc_final: 0.8148 (p) REVERT: 1 70 GLU cc_start: 0.8309 (pm20) cc_final: 0.8073 (pm20) REVERT: K 11 LEU cc_start: 0.8873 (mt) cc_final: 0.8603 (tp) REVERT: K 72 THR cc_start: 0.9005 (m) cc_final: 0.8689 (t) REVERT: K 100 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7138 (t) REVERT: K 140 GLU cc_start: 0.4501 (OUTLIER) cc_final: 0.3875 (pm20) outliers start: 28 outliers final: 18 residues processed: 164 average time/residue: 0.2446 time to fit residues: 51.8607 Evaluate side-chains 153 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 83 ILE 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 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 74 ASN Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET 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 100 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8475 Z= 0.229 Angle : 0.666 9.652 12000 Z= 0.339 Chirality : 0.042 0.308 1460 Planarity : 0.005 0.066 1126 Dihedral : 21.605 178.700 2581 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 5.13 % Allowed : 23.99 % 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: -0.31 (0.31), residues: 734 helix: 0.87 (0.30), residues: 307 sheet: -0.23 (0.45), residues: 135 loop : -1.32 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.012 0.002 HIS 0 60 PHE 0.010 0.001 PHE 0 207 TYR 0.011 0.001 TYR 0 380 ARG 0.003 0.000 ARG K 106 *********************** 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 158 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5491 (mp) REVERT: 0 278 TYR cc_start: 0.8457 (m-10) cc_final: 0.8199 (m-80) REVERT: 0 382 LYS cc_start: 0.8612 (tppt) cc_final: 0.8362 (tppt) REVERT: 0 395 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7471 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9338 (tmtt) cc_final: 0.8688 (tptp) REVERT: 1 17 THR cc_start: 0.8495 (m) cc_final: 0.8168 (p) REVERT: K 11 LEU cc_start: 0.8900 (mt) cc_final: 0.8630 (tp) REVERT: K 72 THR cc_start: 0.9037 (m) cc_final: 0.8743 (t) outliers start: 28 outliers final: 21 residues processed: 148 average time/residue: 0.2339 time to fit residues: 45.2408 Evaluate side-chains 151 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU 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 380 TYR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 74 ASN Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 0.0000 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8475 Z= 0.162 Angle : 0.620 9.492 12000 Z= 0.313 Chirality : 0.040 0.280 1460 Planarity : 0.004 0.061 1126 Dihedral : 21.457 178.043 2581 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.21 % Allowed : 24.73 % Favored : 71.06 % 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: 1.07 (0.30), residues: 303 sheet: -0.11 (0.45), residues: 136 loop : -1.22 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.001 HIS 0 60 PHE 0.008 0.001 PHE 0 297 TYR 0.010 0.001 TYR 0 380 ARG 0.004 0.000 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 155 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.8092 (mmt) cc_final: 0.7190 (mtp) REVERT: 0 240 ILE cc_start: 0.5792 (OUTLIER) cc_final: 0.5509 (mp) REVERT: 0 278 TYR cc_start: 0.8465 (m-10) cc_final: 0.8213 (m-80) REVERT: 0 382 LYS cc_start: 0.8606 (tppt) cc_final: 0.8290 (tppt) REVERT: 0 395 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7418 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9310 (tmtt) cc_final: 0.8666 (tptp) REVERT: 1 14 LYS cc_start: 0.8574 (mptt) cc_final: 0.8186 (mmtp) REVERT: K 11 LEU cc_start: 0.8831 (mt) cc_final: 0.8587 (tp) REVERT: K 64 ARG cc_start: 0.6965 (mtp-110) cc_final: 0.6235 (ttp80) REVERT: K 72 THR cc_start: 0.8972 (m) cc_final: 0.8664 (t) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.2562 time to fit residues: 48.4307 Evaluate side-chains 146 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 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 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.117034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104234 restraints weight = 25848.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107020 restraints weight = 13438.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108295 restraints weight = 6359.523| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8475 Z= 0.190 Angle : 0.637 8.598 12000 Z= 0.322 Chirality : 0.040 0.255 1460 Planarity : 0.004 0.057 1126 Dihedral : 21.493 178.060 2581 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 4.76 % Allowed : 24.73 % Favored : 70.51 % 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: -0.17 (0.31), residues: 734 helix: 1.01 (0.29), residues: 304 sheet: -0.13 (0.45), residues: 136 loop : -1.25 (0.36), residues: 294 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 0.008 0.001 PHE 0 297 TYR 0.010 0.001 TYR 0 380 ARG 0.003 0.000 ARG 0 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.74 seconds wall clock time: 40 minutes 41.44 seconds (2441.44 seconds total)