Starting phenix.real_space_refine on Sun Mar 10 19:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/03_2024/8pkg_17738.pdb" } resolution = 2.99 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2796 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.80, per 1000 atoms: 0.65 Number of scatterers: 4314 At special positions: 0 Unit cell: (78, 82.16, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 804 8.00 N 708 7.00 C 2796 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: 1.71 Conformation dependent library (CDL) restraints added in 785.6 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.331A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.566A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE A 64 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU C 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU B 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL C 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE B 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU D 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU C 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE C 64 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU E 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU D 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL E 65 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE D 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU F 63 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU E 62 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL F 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE E 64 " --> pdb=" O VAL F 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 80 removed outlier: 6.759A pdb=" N THR A 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 75 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 75 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS E 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 75 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS F 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.478A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR E 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE D 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN E 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR F 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 95 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN F 98 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.800A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 105 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR D 105 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR E 105 " --> pdb=" O THR F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.720A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR D 118 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL E 121 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 120 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR E 118 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 120 " --> pdb=" O VAL F 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 90 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 778 1.33 - 1.45: 1124 1.45 - 1.57: 2502 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 4416 Sorted by residual: bond pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.40e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.36e+01 ... (remaining 4411 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.33: 197 106.33 - 113.31: 2336 113.31 - 120.29: 2068 120.29 - 127.28: 1369 127.28 - 134.26: 36 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA SER F 85 " pdb=" C SER F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" CA SER C 85 " pdb=" C SER C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER D 85 " pdb=" C SER D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.54e+01 angle pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.16 121.68 -3.52 7.00e-01 2.04e+00 2.53e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 2166 8.01 - 16.02: 234 16.02 - 24.04: 114 24.04 - 32.05: 54 32.05 - 40.06: 36 Dihedral angle restraints: 2604 sinusoidal: 990 harmonic: 1614 Sorted by residual: dihedral pdb=" C TYR D 116 " pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" CB TYR D 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR A 116 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " pdb=" CB TYR A 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR E 116 " pdb=" N TYR E 116 " pdb=" CA TYR E 116 " pdb=" CB TYR E 116 " ideal model delta harmonic sigma weight residual -122.60 -129.59 6.99 0 2.50e+00 1.60e-01 7.82e+00 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 203 0.058 - 0.115: 247 0.115 - 0.173: 164 0.173 - 0.230: 76 0.230 - 0.287: 18 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE F 107 " pdb=" N ILE F 107 " pdb=" C ILE F 107 " pdb=" CB ILE F 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 114 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C TYR F 114 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR F 114 " 0.016 2.00e-02 2.50e+03 pdb=" N SER F 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS B 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS B 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 91 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS D 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS D 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 91 " 0.015 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 1739 2.90 - 3.40: 3766 3.40 - 3.90: 7659 3.90 - 4.40: 8773 4.40 - 4.90: 16883 Nonbonded interactions: 38820 Sorted by model distance: nonbonded pdb=" O ASN A 27 " pdb=" OH TYR B 69 " model vdw 2.394 2.440 nonbonded pdb=" O ASN B 27 " pdb=" OH TYR C 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN C 27 " pdb=" OH TYR D 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN D 27 " pdb=" OH TYR E 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN E 27 " pdb=" OH TYR F 69 " model vdw 2.395 2.440 ... (remaining 38815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 3.520 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.290 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.012 0.041 4416 Z= 0.848 Angle : 1.652 7.321 6006 Z= 1.222 Chirality : 0.117 0.287 708 Planarity : 0.007 0.034 738 Dihedral : 10.764 40.059 1560 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % 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: -3.24 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.006 0.002 HIS F 31 PHE 0.013 0.002 PHE E 64 TYR 0.007 0.002 TYR B 116 ARG 0.003 0.001 ARG F 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6384 (ttm) cc_final: 0.6072 (ttt) REVERT: A 27 ASN cc_start: 0.7847 (m-40) cc_final: 0.7536 (m110) REVERT: A 34 ARG cc_start: 0.7483 (ttt-90) cc_final: 0.6969 (pmt170) REVERT: A 63 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6692 (tp30) REVERT: A 72 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7139 (pm20) REVERT: A 75 THR cc_start: 0.8487 (m) cc_final: 0.8273 (p) REVERT: A 76 LYS cc_start: 0.8108 (mptt) cc_final: 0.7083 (mmpt) REVERT: A 89 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7038 (pm20) REVERT: B 89 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 13 MET cc_start: 0.6786 (ttm) cc_final: 0.6435 (ttt) REVERT: C 89 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6898 (mt-10) REVERT: D 15 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7513 (mtpp) REVERT: D 63 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6997 (tm-30) REVERT: E 63 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6371 (tp30) REVERT: F 35 LYS cc_start: 0.7428 (tttt) cc_final: 0.6929 (pmtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.9568 time to fit residues: 206.8125 Evaluate side-chains 127 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4416 Z= 0.265 Angle : 0.659 8.592 6006 Z= 0.350 Chirality : 0.051 0.197 708 Planarity : 0.005 0.036 738 Dihedral : 5.165 15.509 594 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.49 % Allowed : 18.59 % 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: -2.76 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS E 31 PHE 0.015 0.002 PHE F 87 TYR 0.027 0.003 TYR F 114 ARG 0.008 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.538 Fit side-chains REVERT: A 13 MET cc_start: 0.6373 (ttm) cc_final: 0.6085 (ttt) REVERT: A 27 ASN cc_start: 0.8036 (m-40) cc_final: 0.7780 (m-40) REVERT: A 34 ARG cc_start: 0.7573 (ttt-90) cc_final: 0.6993 (pmt170) REVERT: A 76 LYS cc_start: 0.8534 (mptt) cc_final: 0.7165 (mmpt) REVERT: A 89 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6985 (pm20) REVERT: B 13 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6367 (tmm) REVERT: B 26 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8271 (mt) REVERT: B 89 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7103 (mt-10) REVERT: C 13 MET cc_start: 0.6705 (ttm) cc_final: 0.6417 (tmm) REVERT: C 89 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6888 (mt-10) REVERT: D 95 PHE cc_start: 0.8413 (t80) cc_final: 0.8196 (t80) REVERT: D 110 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8877 (tp) REVERT: D 112 SER cc_start: 0.9000 (m) cc_final: 0.8700 (m) REVERT: E 13 MET cc_start: 0.6735 (ttp) cc_final: 0.6294 (ttp) REVERT: F 35 LYS cc_start: 0.7463 (tttt) cc_final: 0.7072 (pmtt) REVERT: F 82 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (mt) outliers start: 21 outliers final: 9 residues processed: 138 average time/residue: 0.9154 time to fit residues: 131.8597 Evaluate side-chains 125 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 0.0020 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.229 Angle : 0.591 4.709 6006 Z= 0.312 Chirality : 0.050 0.171 708 Planarity : 0.004 0.024 738 Dihedral : 4.993 17.553 594 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.27 % Allowed : 21.58 % Favored : 74.15 % 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: -2.61 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.002 0.001 HIS F 31 PHE 0.009 0.001 PHE D 64 TYR 0.024 0.002 TYR C 114 ARG 0.004 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.488 Fit side-chains REVERT: A 13 MET cc_start: 0.6414 (ttm) cc_final: 0.6085 (ttm) REVERT: A 34 ARG cc_start: 0.7655 (ttt-90) cc_final: 0.7100 (pmt170) REVERT: A 76 LYS cc_start: 0.8583 (mptt) cc_final: 0.7169 (mmpt) REVERT: A 89 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7058 (pm20) REVERT: B 89 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7074 (mt-10) REVERT: C 13 MET cc_start: 0.6749 (ttm) cc_final: 0.6448 (ttt) REVERT: C 89 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6836 (mt-10) REVERT: D 95 PHE cc_start: 0.8531 (t80) cc_final: 0.8004 (t80) REVERT: D 110 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8893 (tp) REVERT: D 112 SER cc_start: 0.8965 (m) cc_final: 0.8666 (m) REVERT: E 110 LEU cc_start: 0.9191 (tp) cc_final: 0.8989 (tp) REVERT: F 35 LYS cc_start: 0.7525 (tttt) cc_final: 0.6973 (pmtt) REVERT: F 76 LYS cc_start: 0.8343 (mppt) cc_final: 0.6970 (pmtt) outliers start: 20 outliers final: 6 residues processed: 126 average time/residue: 1.0985 time to fit residues: 143.5673 Evaluate side-chains 113 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4416 Z= 0.199 Angle : 0.577 6.619 6006 Z= 0.298 Chirality : 0.049 0.142 708 Planarity : 0.004 0.040 738 Dihedral : 4.963 16.635 594 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.85 % Allowed : 23.29 % Favored : 72.86 % 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: -2.55 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 79 HIS 0.002 0.000 HIS E 31 PHE 0.008 0.001 PHE D 64 TYR 0.023 0.002 TYR E 114 ARG 0.009 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.489 Fit side-chains REVERT: A 13 MET cc_start: 0.6278 (ttm) cc_final: 0.6024 (ttm) REVERT: A 34 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.7220 (pmt170) REVERT: A 63 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7233 (tm-30) REVERT: A 76 LYS cc_start: 0.8602 (mptt) cc_final: 0.7197 (mmpt) REVERT: B 13 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6108 (ttm) REVERT: B 89 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7130 (mt-10) REVERT: C 13 MET cc_start: 0.6666 (ttm) cc_final: 0.6318 (tmm) REVERT: C 21 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6231 (tpp-160) REVERT: C 89 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6884 (mt-10) REVERT: D 112 SER cc_start: 0.8941 (m) cc_final: 0.8673 (m) REVERT: D 117 SER cc_start: 0.8991 (m) cc_final: 0.8700 (m) REVERT: E 110 LEU cc_start: 0.9122 (tp) cc_final: 0.8809 (tp) REVERT: F 26 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7000 (tp) REVERT: F 35 LYS cc_start: 0.7537 (tttt) cc_final: 0.6901 (pmtt) REVERT: F 76 LYS cc_start: 0.8291 (mppt) cc_final: 0.6899 (pmtt) outliers start: 18 outliers final: 7 residues processed: 125 average time/residue: 1.1101 time to fit residues: 143.9672 Evaluate side-chains 112 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 27 ASN B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 4416 Z= 0.391 Angle : 0.688 6.621 6006 Z= 0.361 Chirality : 0.051 0.138 708 Planarity : 0.005 0.033 738 Dihedral : 5.432 18.528 594 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.49 % Allowed : 23.50 % Favored : 72.01 % 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: -2.48 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.005 0.001 HIS F 31 PHE 0.014 0.002 PHE A 87 TYR 0.020 0.002 TYR C 114 ARG 0.005 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.538 Fit side-chains REVERT: A 13 MET cc_start: 0.6367 (ttm) cc_final: 0.6087 (ttm) REVERT: A 34 ARG cc_start: 0.7745 (ttt-90) cc_final: 0.7163 (pmt170) REVERT: A 63 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7250 (tp30) REVERT: A 76 LYS cc_start: 0.8552 (mptt) cc_final: 0.7025 (mmpt) REVERT: B 89 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 13 MET cc_start: 0.6599 (ttm) cc_final: 0.6359 (tmt) REVERT: C 15 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7819 (ttmp) REVERT: C 21 ARG cc_start: 0.7149 (tpp80) cc_final: 0.6397 (tpp-160) REVERT: C 34 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7438 (ttt-90) REVERT: E 110 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8819 (tp) REVERT: F 26 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7498 (tp) REVERT: F 35 LYS cc_start: 0.7897 (tttt) cc_final: 0.7119 (pmtt) outliers start: 21 outliers final: 9 residues processed: 114 average time/residue: 1.2688 time to fit residues: 149.3971 Evaluate side-chains 103 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4416 Z= 0.278 Angle : 0.626 7.452 6006 Z= 0.322 Chirality : 0.050 0.128 708 Planarity : 0.004 0.031 738 Dihedral : 5.321 17.903 594 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.85 % Allowed : 23.72 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.011 0.001 PHE A 87 TYR 0.019 0.002 TYR C 114 ARG 0.004 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.454 Fit side-chains REVERT: A 13 MET cc_start: 0.6406 (ttm) cc_final: 0.6062 (ttm) REVERT: A 34 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7108 (pmt170) REVERT: A 70 LYS cc_start: 0.6616 (pmtt) cc_final: 0.6400 (pptt) REVERT: A 76 LYS cc_start: 0.8519 (mptt) cc_final: 0.6987 (mmpt) REVERT: B 89 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 21 ARG cc_start: 0.7119 (tpp80) cc_final: 0.6368 (tpp-160) REVERT: C 89 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7250 (mt-10) REVERT: C 100 SER cc_start: 0.5890 (p) cc_final: 0.5615 (p) REVERT: F 26 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7461 (tp) REVERT: F 35 LYS cc_start: 0.7881 (tttt) cc_final: 0.7084 (pmtt) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 1.3184 time to fit residues: 148.3606 Evaluate side-chains 98 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4416 Z= 0.211 Angle : 0.599 9.785 6006 Z= 0.303 Chirality : 0.049 0.128 708 Planarity : 0.004 0.043 738 Dihedral : 5.102 18.735 594 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.78 % Allowed : 24.36 % Favored : 72.86 % 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: -2.47 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.002 0.000 HIS E 31 PHE 0.007 0.001 PHE A 87 TYR 0.018 0.001 TYR C 114 ARG 0.011 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.526 Fit side-chains REVERT: A 13 MET cc_start: 0.6327 (ttm) cc_final: 0.6108 (ttm) REVERT: A 34 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.7091 (pmt170) REVERT: A 63 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7094 (tp30) REVERT: A 70 LYS cc_start: 0.6610 (pmtt) cc_final: 0.6396 (pptt) REVERT: A 76 LYS cc_start: 0.8538 (mptt) cc_final: 0.7030 (mmpt) REVERT: B 89 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7497 (mt-10) REVERT: C 21 ARG cc_start: 0.7069 (tpp80) cc_final: 0.6438 (tpp-160) REVERT: C 34 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7308 (ttt-90) REVERT: C 89 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7184 (mt-10) REVERT: F 13 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6832 (ttp) REVERT: F 26 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7055 (tp) REVERT: F 35 LYS cc_start: 0.7695 (tttt) cc_final: 0.6986 (pmtt) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 1.3002 time to fit residues: 139.5905 Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4416 Z= 0.256 Angle : 0.621 8.935 6006 Z= 0.316 Chirality : 0.049 0.133 708 Planarity : 0.004 0.043 738 Dihedral : 5.199 18.120 594 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.99 % Allowed : 23.72 % Favored : 73.29 % 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: -2.49 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 79 HIS 0.003 0.001 HIS E 31 PHE 0.012 0.002 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.010 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.533 Fit side-chains REVERT: A 34 ARG cc_start: 0.7622 (ttt-90) cc_final: 0.7087 (pmt170) REVERT: A 63 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7083 (tp30) REVERT: A 76 LYS cc_start: 0.8559 (mptt) cc_final: 0.7005 (mmpt) REVERT: B 89 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 21 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6477 (tpp-160) REVERT: C 34 ARG cc_start: 0.7626 (ttt-90) cc_final: 0.7369 (ttt-90) REVERT: D 21 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6821 (ttp80) REVERT: D 112 SER cc_start: 0.8905 (m) cc_final: 0.8576 (m) REVERT: F 13 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6849 (ttp) REVERT: F 26 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7086 (tp) REVERT: F 35 LYS cc_start: 0.7752 (tttt) cc_final: 0.6916 (pmtt) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 1.2990 time to fit residues: 143.5234 Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4416 Z= 0.224 Angle : 0.599 8.939 6006 Z= 0.302 Chirality : 0.049 0.129 708 Planarity : 0.004 0.037 738 Dihedral : 5.100 17.575 594 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.35 % Allowed : 23.93 % Favored : 73.72 % 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: -2.47 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 PHE 0.008 0.001 PHE A 87 TYR 0.018 0.001 TYR C 114 ARG 0.009 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.511 Fit side-chains REVERT: A 34 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.7088 (pmt170) REVERT: A 63 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7142 (tp30) REVERT: A 76 LYS cc_start: 0.8556 (mptt) cc_final: 0.6992 (mmpt) REVERT: B 89 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 110 LEU cc_start: 0.8632 (tt) cc_final: 0.8372 (tt) REVERT: C 21 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6516 (tpp-160) REVERT: C 34 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7421 (ttt-90) REVERT: C 99 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6346 (t0) REVERT: D 112 SER cc_start: 0.8867 (m) cc_final: 0.8611 (m) REVERT: F 13 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6848 (ttp) REVERT: F 26 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7056 (tp) REVERT: F 35 LYS cc_start: 0.7788 (tttt) cc_final: 0.6898 (pmtt) outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 1.2853 time to fit residues: 136.7970 Evaluate side-chains 99 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4416 Z= 0.217 Angle : 0.630 12.508 6006 Z= 0.309 Chirality : 0.049 0.125 708 Planarity : 0.004 0.049 738 Dihedral : 5.043 17.175 594 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 23.93 % Favored : 73.50 % 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: -2.46 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 PHE 0.008 0.001 PHE A 87 TYR 0.018 0.001 TYR C 114 ARG 0.011 0.001 ARG E 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.527 Fit side-chains REVERT: A 34 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.7087 (pmt170) REVERT: A 63 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7126 (tp30) REVERT: A 76 LYS cc_start: 0.8589 (mptt) cc_final: 0.7047 (mmpt) REVERT: B 89 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 110 LEU cc_start: 0.8736 (tt) cc_final: 0.8372 (tt) REVERT: C 21 ARG cc_start: 0.7303 (tpp80) cc_final: 0.6607 (tpp-160) REVERT: C 23 SER cc_start: 0.7998 (m) cc_final: 0.7688 (m) REVERT: C 34 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.7420 (ttt-90) REVERT: C 99 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6343 (t0) REVERT: D 21 ARG cc_start: 0.7058 (tpp80) cc_final: 0.6774 (ttp80) REVERT: D 112 SER cc_start: 0.8869 (m) cc_final: 0.8611 (m) REVERT: F 13 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6836 (ttp) REVERT: F 26 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7054 (tp) REVERT: F 35 LYS cc_start: 0.7806 (tttt) cc_final: 0.6920 (pmtt) outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 1.2936 time to fit residues: 133.6026 Evaluate side-chains 103 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 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 = 0.4161 r_free = 0.4161 target = 0.121407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.104354 restraints weight = 6678.894| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.63 r_work: 0.3900 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4416 Z= 0.214 Angle : 0.618 11.556 6006 Z= 0.304 Chirality : 0.049 0.125 708 Planarity : 0.004 0.035 738 Dihedral : 4.997 17.136 594 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.14 % Allowed : 24.36 % Favored : 73.50 % 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: -2.43 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.008 0.001 PHE A 87 TYR 0.018 0.001 TYR C 114 ARG 0.008 0.001 ARG C 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.66 seconds wall clock time: 48 minutes 39.87 seconds (2919.87 seconds total)