Starting phenix.real_space_refine on Sat Dec 9 08:45:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyj_27080/12_2023/8cyj_27080.pdb" } resolution = 3.6 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= 0.017 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 S 26 5.16 5 C 3454 2.51 5 N 940 2.21 5 O 1066 1.98 5 H 5089 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10575 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1908 Classifications: {'peptide': 127} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1883 Classifications: {'peptide': 125} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1945 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1885 Classifications: {'peptide': 127} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "R" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2954 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 5.22, per 1000 atoms: 0.49 Number of scatterers: 10575 At special positions: 0 Unit cell: (68.552, 107.008, 125.4, 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 26 16.00 O 1066 8.00 N 940 7.00 C 3454 6.00 H 5089 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 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: 8.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 9.3% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.707A pdb=" N LYS A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.779A pdb=" N THR D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.857A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE R 342 " --> pdb=" O PHE R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 405 through 410 Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.207A pdb=" N GLY A 10 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.207A pdb=" N GLY A 10 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 101 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 116 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.292A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N SER B 124 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 12 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N TYR B 32 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 52 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.292A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N SER B 124 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 12 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 98 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR B 114 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.923A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.923A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR C 117 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.832A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 452 through 454 206 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5089 1.03 - 1.23: 0 1.23 - 1.42: 2555 1.42 - 1.62: 3027 1.62 - 1.81: 36 Bond restraints: 10707 Sorted by residual: bond pdb=" CB PRO R 463 " pdb=" CG PRO R 463 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.91e+00 bond pdb=" CG PRO R 463 " pdb=" CD PRO R 463 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.19e+00 bond pdb=" CB MET B 78 " pdb=" CG MET B 78 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.70e-01 bond pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.21e-02 6.83e+03 7.62e-01 ... (remaining 10702 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.78: 80 105.78 - 112.83: 11473 112.83 - 119.89: 3064 119.89 - 126.95: 4403 126.95 - 134.01: 56 Bond angle restraints: 19076 Sorted by residual: angle pdb=" C ALA R 475 " pdb=" CA ALA R 475 " pdb=" CB ALA R 475 " ideal model delta sigma weight residual 115.79 109.92 5.87 1.19e+00 7.06e-01 2.44e+01 angle pdb=" N SER R 477 " pdb=" CA SER R 477 " pdb=" C SER R 477 " ideal model delta sigma weight residual 114.75 110.21 4.54 1.26e+00 6.30e-01 1.30e+01 angle pdb=" N ARG B 67 " pdb=" CA ARG B 67 " pdb=" C ARG B 67 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.95e+00 angle pdb=" N ASP C 105 " pdb=" CA ASP C 105 " pdb=" C ASP C 105 " ideal model delta sigma weight residual 107.93 113.04 -5.11 1.65e+00 3.67e-01 9.59e+00 angle pdb=" CA PRO R 463 " pdb=" N PRO R 463 " pdb=" CD PRO R 463 " ideal model delta sigma weight residual 112.00 107.95 4.05 1.40e+00 5.10e-01 8.37e+00 ... (remaining 19071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4620 17.32 - 34.63: 304 34.63 - 51.95: 49 51.95 - 69.27: 13 69.27 - 86.59: 14 Dihedral angle restraints: 5000 sinusoidal: 2526 harmonic: 2474 Sorted by residual: dihedral pdb=" CA HIS C 103 " pdb=" C HIS C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N GLY D 109 " pdb=" CA GLY D 109 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLY D 109 " pdb=" C GLY D 109 " pdb=" N ASN D 110 " pdb=" CA ASN D 110 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 4997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 543 0.035 - 0.070: 174 0.070 - 0.105: 45 0.105 - 0.141: 30 0.141 - 0.176: 1 Chirality restraints: 793 Sorted by residual: chirality pdb=" CA PRO R 463 " pdb=" N PRO R 463 " pdb=" C PRO R 463 " pdb=" CB PRO R 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE R 434 " pdb=" N ILE R 434 " pdb=" C ILE R 434 " pdb=" CB ILE R 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL C 124 " pdb=" N VAL C 124 " pdb=" C VAL C 124 " pdb=" CB VAL C 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 790 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO R 463 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 75 " -0.214 9.50e-02 1.11e+02 7.17e-02 6.21e+00 pdb=" NE ARG A 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 75 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 75 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 75 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 75 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 75 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 75 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 75 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO R 491 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.034 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 387 2.15 - 2.77: 19600 2.77 - 3.38: 28501 3.38 - 3.99: 38687 3.99 - 4.60: 58143 Nonbonded interactions: 145318 Sorted by model distance: nonbonded pdb=" OE1 GLN A 119 " pdb=" H GLN A 119 " model vdw 1.543 1.850 nonbonded pdb=" O VAL A 105 " pdb=" HH TYR R 489 " model vdw 1.659 1.850 nonbonded pdb=" O ARG C 31 " pdb=" H HIS C 103 " model vdw 1.703 1.850 nonbonded pdb="HH12 ARG B 38 " pdb=" OE1 GLU B 89 " model vdw 1.710 1.850 nonbonded pdb=" O TYR C 52 " pdb="HH11 ARG C 72 " model vdw 1.714 1.850 ... (remaining 145313 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: 0.920 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: 0.160 Extract box with map and model: 4.190 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 5618 Z= 0.180 Angle : 0.619 6.883 7616 Z= 0.375 Chirality : 0.042 0.176 793 Planarity : 0.006 0.131 996 Dihedral : 14.181 86.585 1988 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.66 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.91 (0.31), residues: 691 helix: -2.74 (0.94), residues: 20 sheet: 0.34 (0.31), residues: 236 loop : -1.07 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 53 HIS 0.001 0.000 HIS D 113 PHE 0.009 0.001 PHE B 29 TYR 0.006 0.001 TYR D 114 ARG 0.014 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.904 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.5030 time to fit residues: 56.9590 Evaluate side-chains 81 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 5618 Z= 0.278 Angle : 0.631 7.020 7616 Z= 0.348 Chirality : 0.045 0.192 793 Planarity : 0.006 0.129 996 Dihedral : 5.666 33.097 789 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 1.01 % Allowed : 7.53 % Favored : 91.46 % Rotamer: Outliers : 1.55 % Allowed : 6.04 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.31), residues: 691 helix: -4.38 (1.07), residues: 8 sheet: 0.25 (0.31), residues: 248 loop : -1.29 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 53 HIS 0.002 0.001 HIS D 113 PHE 0.016 0.002 PHE R 377 TYR 0.018 0.002 TYR B 112 ARG 0.007 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.808 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.5283 time to fit residues: 57.8890 Evaluate side-chains 81 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1252 time to fit residues: 2.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 5618 Z= 0.192 Angle : 0.540 6.649 7616 Z= 0.293 Chirality : 0.043 0.183 793 Planarity : 0.005 0.126 996 Dihedral : 5.384 33.970 789 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.80 % Favored : 92.33 % Rotamer: Outliers : 0.86 % Allowed : 10.54 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 691 helix: -4.46 (1.00), residues: 8 sheet: 0.13 (0.32), residues: 249 loop : -1.23 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 PHE 0.021 0.002 PHE R 338 TYR 0.012 0.001 TYR D 114 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.983 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 0.5308 time to fit residues: 51.8422 Evaluate side-chains 76 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1648 time to fit residues: 1.9381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 5618 Z= 0.239 Angle : 0.571 6.650 7616 Z= 0.311 Chirality : 0.043 0.183 793 Planarity : 0.005 0.125 996 Dihedral : 5.450 32.827 789 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.54 % Favored : 90.59 % Rotamer: Outliers : 1.55 % Allowed : 10.88 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.32), residues: 691 helix: -4.58 (0.88), residues: 8 sheet: 0.05 (0.32), residues: 261 loop : -1.34 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.004 0.002 HIS R 519 PHE 0.014 0.002 PHE R 377 TYR 0.013 0.002 TYR C 106 ARG 0.004 0.001 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.980 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: symmetry clash 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: symmetry clash outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.5192 time to fit residues: 51.3904 Evaluate side-chains 78 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1423 time to fit residues: 2.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 5618 Z= 0.266 Angle : 0.596 6.439 7616 Z= 0.328 Chirality : 0.044 0.180 793 Planarity : 0.005 0.124 996 Dihedral : 5.669 35.487 789 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.41 % Favored : 89.73 % Rotamer: Outliers : 2.42 % Allowed : 11.92 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 691 helix: -4.67 (0.81), residues: 8 sheet: 0.00 (0.33), residues: 246 loop : -1.56 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.005 0.002 HIS R 519 PHE 0.015 0.002 PHE R 377 TYR 0.017 0.002 TYR C 106 ARG 0.004 0.001 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.853 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: symmetry clash 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: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 85 average time/residue: 0.5014 time to fit residues: 52.4799 Evaluate side-chains 76 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1953 time to fit residues: 3.1148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5618 Z= 0.212 Angle : 0.556 6.303 7616 Z= 0.301 Chirality : 0.043 0.178 793 Planarity : 0.005 0.123 996 Dihedral : 5.522 33.108 789 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.83 % Favored : 90.45 % Rotamer: Outliers : 1.04 % Allowed : 13.13 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.32), residues: 691 helix: -4.69 (0.79), residues: 8 sheet: -0.12 (0.33), residues: 254 loop : -1.52 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 PHE 0.031 0.002 PHE D 29 TYR 0.013 0.001 TYR D 114 ARG 0.004 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.874 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: symmetry clash 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: symmetry clash outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.5196 time to fit residues: 45.9725 Evaluate side-chains 73 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.819 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1206 time to fit residues: 1.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 5618 Z= 0.261 Angle : 0.589 6.227 7616 Z= 0.323 Chirality : 0.044 0.179 793 Planarity : 0.005 0.122 996 Dihedral : 5.718 35.638 789 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.56 % Favored : 88.71 % Rotamer: Outliers : 1.21 % Allowed : 13.99 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.32), residues: 691 helix: -4.81 (0.67), residues: 8 sheet: -0.03 (0.33), residues: 251 loop : -1.59 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.005 0.002 HIS B 59 PHE 0.022 0.002 PHE D 29 TYR 0.014 0.002 TYR D 114 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.896 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.4882 time to fit residues: 42.9264 Evaluate side-chains 67 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.880 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1391 time to fit residues: 2.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 5618 Z= 0.199 Angle : 0.558 6.494 7616 Z= 0.302 Chirality : 0.044 0.173 793 Planarity : 0.005 0.120 996 Dihedral : 5.488 32.917 789 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.26 % Favored : 90.01 % Rotamer: Outliers : 0.69 % Allowed : 14.68 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.32), residues: 691 helix: -4.81 (0.68), residues: 8 sheet: -0.05 (0.33), residues: 254 loop : -1.53 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.004 0.001 HIS C 103 PHE 0.022 0.002 PHE D 29 TYR 0.013 0.001 TYR D 114 ARG 0.006 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.873 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: symmetry clash 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: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.5025 time to fit residues: 45.5727 Evaluate side-chains 70 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.950 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1300 time to fit residues: 1.6747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 5618 Z= 0.203 Angle : 0.564 5.814 7616 Z= 0.306 Chirality : 0.043 0.173 793 Planarity : 0.005 0.119 996 Dihedral : 5.466 35.694 789 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.99 % Favored : 89.29 % Rotamer: Outliers : 0.35 % Allowed : 15.37 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.33), residues: 691 helix: -4.76 (0.72), residues: 8 sheet: -0.07 (0.33), residues: 255 loop : -1.51 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 PHE 0.019 0.002 PHE D 29 TYR 0.014 0.001 TYR D 114 ARG 0.007 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.959 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.5235 time to fit residues: 44.6086 Evaluate side-chains 70 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1232 time to fit residues: 1.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 5618 Z= 0.214 Angle : 0.566 5.898 7616 Z= 0.306 Chirality : 0.044 0.172 793 Planarity : 0.005 0.118 996 Dihedral : 5.467 33.497 789 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.42 % Favored : 88.86 % Rotamer: Outliers : 0.17 % Allowed : 15.89 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.33), residues: 691 helix: -4.82 (0.68), residues: 8 sheet: -0.08 (0.34), residues: 255 loop : -1.51 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.003 0.001 HIS B 59 PHE 0.019 0.002 PHE D 29 TYR 0.015 0.001 TYR D 114 ARG 0.006 0.001 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.896 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.4880 time to fit residues: 41.3954 Evaluate side-chains 64 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** 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 = 0.4558 r_free = 0.4558 target = 0.106311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.094064 restraints weight = 89709.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.096858 restraints weight = 45673.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.098563 restraints weight = 28612.396| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 5618 Z= 0.269 Angle : 0.608 6.021 7616 Z= 0.333 Chirality : 0.044 0.175 793 Planarity : 0.006 0.117 996 Dihedral : 5.793 36.265 789 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.16 % Favored : 87.12 % Rotamer: Outliers : 0.35 % Allowed : 16.06 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.33), residues: 691 helix: -4.92 (0.59), residues: 8 sheet: -0.22 (0.34), residues: 255 loop : -1.64 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 HIS 0.005 0.002 HIS B 59 PHE 0.016 0.002 PHE D 29 TYR 0.017 0.002 TYR D 114 ARG 0.005 0.001 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.23 seconds wall clock time: 59 minutes 9.10 seconds (3549.10 seconds total)