Starting phenix.real_space_refine on Tue Feb 13 06:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7d_26587/02_2024/8e7d_26587.pdb" } resolution = 3.31 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= 0.003 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 5 5.16 5 C 2285 2.51 5 N 575 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3525 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "B" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "E" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Time building chain proxies: 2.56, per 1000 atoms: 0.73 Number of scatterers: 3525 At special positions: 0 Unit cell: (71.02, 83.74, 40.28, 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 5 16.00 O 660 8.00 N 575 7.00 C 2285 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: 1.41 Conformation dependent library (CDL) restraints added in 677.5 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 51.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.787A pdb=" N MET B 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL D 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20 removed outlier: 6.762A pdb=" N ALA B 19 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.414A pdb=" N ALA B 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.270A pdb=" N VAL A 30 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 32 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE E 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 73 removed outlier: 6.917A pdb=" N GLU B 61 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU D 62 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU B 63 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B 67 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 68 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 61 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 63 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY A 67 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 68 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N THR A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N GLU C 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU A 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL C 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY C 67 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU A 66 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N TYR C 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 68 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE C 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLU E 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL E 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY E 67 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU C 66 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE C 68 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 71 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE E 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80 removed outlier: 6.989A pdb=" N SER B 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR D 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS C 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N TRP E 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 99 removed outlier: 6.913A pdb=" N HIS A 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL C 93 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A 92 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE C 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 94 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 96 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP C 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A 98 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS C 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL E 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU C 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE E 95 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA E 97 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 96 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASP E 99 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 98 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.612A pdb=" N ARG B 103 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR D 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR B 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 103 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR B 106 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 121 removed outlier: 6.795A pdb=" N SER D 115 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER B 115 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 115 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR C 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 117 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA C 120 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 119 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER C 115 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR E 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 117 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA E 120 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 119 " --> pdb=" O ALA E 120 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 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: 0.86 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1031 1.33 - 1.45: 564 1.45 - 1.57: 2005 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 3610 Sorted by residual: bond pdb=" CA TYR E 116 " pdb=" C TYR E 116 " ideal model delta sigma weight residual 1.520 1.480 0.041 1.17e-02 7.31e+03 1.22e+01 bond pdb=" CA TYR C 116 " pdb=" C TYR C 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" CA TYR B 116 " pdb=" C TYR B 116 " ideal model delta sigma weight residual 1.520 1.481 0.040 1.17e-02 7.31e+03 1.15e+01 bond pdb=" CA TYR A 116 " pdb=" C TYR A 116 " ideal model delta sigma weight residual 1.520 1.481 0.040 1.17e-02 7.31e+03 1.15e+01 ... (remaining 3605 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.24: 185 107.24 - 113.93: 2025 113.93 - 120.62: 1381 120.62 - 127.32: 1289 127.32 - 134.01: 40 Bond angle restraints: 4920 Sorted by residual: angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" CA TYR E 114 " pdb=" CB TYR E 114 " pdb=" CG TYR E 114 " ideal model delta sigma weight residual 113.90 118.14 -4.24 1.80e+00 3.09e-01 5.54e+00 angle pdb=" CA TYR D 114 " pdb=" CB TYR D 114 " pdb=" CG TYR D 114 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.51e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.51e+00 ... (remaining 4915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 1755 16.88 - 33.76: 270 33.76 - 50.64: 85 50.64 - 67.52: 10 67.52 - 84.40: 5 Dihedral angle restraints: 2125 sinusoidal: 800 harmonic: 1325 Sorted by residual: dihedral pdb=" CA PHE C 87 " pdb=" C PHE C 87 " pdb=" N HIS C 88 " pdb=" CA HIS C 88 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE E 87 " pdb=" C PHE E 87 " pdb=" N HIS E 88 " pdb=" CA HIS E 88 " ideal model delta harmonic sigma weight residual 180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE A 87 " pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 364 0.041 - 0.082: 118 0.082 - 0.123: 88 0.123 - 0.164: 10 0.164 - 0.205: 5 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA PRO C 86 " pdb=" N PRO C 86 " pdb=" C PRO C 86 " pdb=" CB PRO C 86 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 86 " pdb=" N PRO A 86 " pdb=" C PRO A 86 " pdb=" CB PRO A 86 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" C PRO D 86 " pdb=" CB PRO D 86 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 582 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " 0.056 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 82 2.67 - 3.23: 3305 3.23 - 3.79: 5427 3.79 - 4.34: 7566 4.34 - 4.90: 13516 Nonbonded interactions: 29896 Sorted by model distance: nonbonded pdb=" O VAL E 28 " pdb=" OH TYR E 69 " model vdw 2.117 2.440 nonbonded pdb=" O VAL C 28 " pdb=" OH TYR C 69 " model vdw 2.117 2.440 nonbonded pdb=" O VAL B 28 " pdb=" OH TYR B 69 " model vdw 2.117 2.440 nonbonded pdb=" O VAL D 28 " pdb=" OH TYR D 69 " model vdw 2.117 2.440 nonbonded pdb=" O VAL A 28 " pdb=" OH TYR A 69 " model vdw 2.118 2.440 ... (remaining 29891 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' } 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: 0.670 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: 3.510 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.005 0.051 3610 Z= 0.351 Angle : 0.703 4.253 4920 Z= 0.414 Chirality : 0.056 0.205 585 Planarity : 0.010 0.104 605 Dihedral : 18.191 84.395 1265 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.26 % Allowed : 37.40 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.27), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.20), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP E 79 HIS 0.003 0.001 HIS B 88 PHE 0.014 0.003 PHE A 95 TYR 0.012 0.002 TYR D 105 ARG 0.005 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.426 Fit side-chains REVERT: B 99 ASP cc_start: 0.7720 (t0) cc_final: 0.7469 (t0) REVERT: C 89 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 99 ASP cc_start: 0.7656 (t0) cc_final: 0.7369 (t0) REVERT: D 13 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: D 99 ASP cc_start: 0.6627 (t0) cc_final: 0.6396 (p0) REVERT: D 114 TYR cc_start: 0.8409 (p90) cc_final: 0.5504 (m-10) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1149 time to fit residues: 16.2793 Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 3610 Z= 0.566 Angle : 0.751 8.100 4920 Z= 0.417 Chirality : 0.054 0.183 585 Planarity : 0.007 0.060 605 Dihedral : 6.449 17.009 488 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 8.05 % Allowed : 30.13 % Favored : 61.82 % 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: -4.26 (0.31), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.006 0.002 HIS D 31 PHE 0.026 0.003 PHE A 33 TYR 0.030 0.003 TYR A 114 ARG 0.003 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 0.433 Fit side-chains REVERT: A 13 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7594 (tmm) REVERT: B 13 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7321 (tmm) REVERT: B 89 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 99 ASP cc_start: 0.7577 (t0) cc_final: 0.7217 (t0) REVERT: B 103 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7745 (mtm-85) REVERT: C 13 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7425 (tmm) REVERT: C 63 GLU cc_start: 0.8206 (mp0) cc_final: 0.7834 (mp0) REVERT: C 89 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 99 ASP cc_start: 0.7603 (t0) cc_final: 0.6960 (t0) REVERT: C 103 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8110 (mtm-85) REVERT: C 112 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8568 (m) REVERT: D 13 MET cc_start: 0.8121 (ttm) cc_final: 0.7743 (tmm) REVERT: D 89 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 115 SER cc_start: 0.8210 (m) cc_final: 0.7942 (t) REVERT: E 103 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8191 (mtt180) outliers start: 31 outliers final: 15 residues processed: 93 average time/residue: 0.1348 time to fit residues: 15.7740 Evaluate side-chains 94 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3610 Z= 0.214 Angle : 0.605 8.728 4920 Z= 0.326 Chirality : 0.051 0.145 585 Planarity : 0.005 0.040 605 Dihedral : 5.819 15.021 485 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.97 % Allowed : 30.13 % Favored : 63.90 % 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: -4.20 (0.31), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.001 0.000 HIS E 88 PHE 0.017 0.002 PHE A 33 TYR 0.028 0.002 TYR A 114 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.468 Fit side-chains REVERT: A 13 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: A 103 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7272 (mtt180) REVERT: B 13 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7430 (tmm) REVERT: B 99 ASP cc_start: 0.7345 (t0) cc_final: 0.7013 (t70) REVERT: B 103 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7675 (mtm180) REVERT: C 99 ASP cc_start: 0.7267 (t0) cc_final: 0.6881 (t0) REVERT: C 103 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8188 (mtm-85) REVERT: C 112 SER cc_start: 0.8916 (p) cc_final: 0.8614 (m) REVERT: D 13 MET cc_start: 0.8027 (ttm) cc_final: 0.7743 (tmm) REVERT: E 13 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7558 (tmm) REVERT: E 74 ASP cc_start: 0.8442 (t70) cc_final: 0.7882 (t70) REVERT: E 88 HIS cc_start: 0.8230 (t-170) cc_final: 0.6749 (p-80) REVERT: E 95 PHE cc_start: 0.8764 (t80) cc_final: 0.8451 (t80) REVERT: E 103 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.5763 (mmp-170) outliers start: 23 outliers final: 8 residues processed: 97 average time/residue: 0.1619 time to fit residues: 19.2812 Evaluate side-chains 86 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 103 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** 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: 0.7995 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3610 Z= 0.470 Angle : 0.702 8.757 4920 Z= 0.378 Chirality : 0.052 0.148 585 Planarity : 0.005 0.032 605 Dihedral : 5.890 17.646 485 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 9.35 % Allowed : 26.49 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.005 0.001 HIS A 31 PHE 0.020 0.003 PHE B 33 TYR 0.025 0.003 TYR E 114 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7547 (tmm) REVERT: A 103 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7861 (mtt180) REVERT: B 13 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7413 (tmm) REVERT: B 103 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6788 (mtt90) REVERT: D 13 MET cc_start: 0.8399 (ttm) cc_final: 0.8008 (tmm) REVERT: D 103 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7389 (mtt90) REVERT: E 103 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8198 (mtt180) outliers start: 36 outliers final: 22 residues processed: 90 average time/residue: 0.1547 time to fit residues: 17.1148 Evaluate side-chains 95 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3610 Z= 0.228 Angle : 0.623 8.350 4920 Z= 0.331 Chirality : 0.051 0.133 585 Planarity : 0.004 0.027 605 Dihedral : 5.601 16.598 485 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.71 % Allowed : 29.87 % Favored : 64.42 % 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: -4.06 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.001 0.000 HIS A 31 PHE 0.016 0.002 PHE B 33 TYR 0.023 0.002 TYR A 114 ARG 0.002 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7486 (tmm) REVERT: A 103 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: B 13 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7434 (tmm) REVERT: B 99 ASP cc_start: 0.7363 (t0) cc_final: 0.6229 (t0) REVERT: B 103 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6818 (mtt90) REVERT: C 110 LEU cc_start: 0.9295 (tt) cc_final: 0.9062 (tt) REVERT: C 112 SER cc_start: 0.8883 (p) cc_final: 0.8632 (m) REVERT: D 13 MET cc_start: 0.8336 (ttm) cc_final: 0.8025 (tmm) REVERT: D 103 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7426 (mtt180) REVERT: E 13 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7554 (tmm) REVERT: E 74 ASP cc_start: 0.8359 (t70) cc_final: 0.7850 (t70) REVERT: E 95 PHE cc_start: 0.8760 (t80) cc_final: 0.8408 (t80) REVERT: E 103 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.5870 (mmp-170) outliers start: 22 outliers final: 11 residues processed: 85 average time/residue: 0.1462 time to fit residues: 15.4806 Evaluate side-chains 84 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 3610 Z= 0.526 Angle : 0.712 8.715 4920 Z= 0.384 Chirality : 0.052 0.147 585 Planarity : 0.004 0.026 605 Dihedral : 5.795 17.095 485 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 9.61 % Allowed : 25.97 % Favored : 64.42 % 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: -3.91 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.006 0.002 HIS A 31 PHE 0.017 0.002 PHE B 33 TYR 0.024 0.003 TYR E 114 ARG 0.004 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 68 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7407 (tmm) REVERT: A 103 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7941 (mtt180) REVERT: B 13 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7504 (tmm) REVERT: C 112 SER cc_start: 0.8877 (p) cc_final: 0.8569 (m) REVERT: D 13 MET cc_start: 0.8357 (ttm) cc_final: 0.8024 (tmm) REVERT: D 103 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7650 (mtt90) REVERT: E 13 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7612 (tmm) REVERT: E 74 ASP cc_start: 0.8383 (t70) cc_final: 0.7823 (t70) REVERT: E 103 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.5971 (mmp-170) outliers start: 37 outliers final: 26 residues processed: 88 average time/residue: 0.1578 time to fit residues: 16.9454 Evaluate side-chains 95 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3610 Z= 0.236 Angle : 0.656 8.859 4920 Z= 0.341 Chirality : 0.051 0.130 585 Planarity : 0.004 0.027 605 Dihedral : 5.596 19.729 485 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 6.75 % Allowed : 29.09 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.001 0.000 HIS A 31 PHE 0.020 0.002 PHE C 33 TYR 0.022 0.002 TYR A 114 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7516 (tmm) REVERT: A 103 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7795 (mtt180) REVERT: B 13 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7465 (tmm) REVERT: B 99 ASP cc_start: 0.7308 (t0) cc_final: 0.6064 (t0) REVERT: B 103 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6658 (mtt90) REVERT: D 13 MET cc_start: 0.8338 (ttm) cc_final: 0.8043 (tmm) REVERT: D 103 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7585 (mtt180) REVERT: E 13 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7576 (tmm) REVERT: E 74 ASP cc_start: 0.8204 (t70) cc_final: 0.7723 (t70) REVERT: E 95 PHE cc_start: 0.8749 (t80) cc_final: 0.8417 (t80) REVERT: E 103 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.5877 (mmp-170) outliers start: 26 outliers final: 15 residues processed: 89 average time/residue: 0.1582 time to fit residues: 17.3742 Evaluate side-chains 89 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 103 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3610 Z= 0.388 Angle : 0.689 8.757 4920 Z= 0.364 Chirality : 0.051 0.138 585 Planarity : 0.004 0.024 605 Dihedral : 5.622 20.318 485 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 8.57 % Allowed : 26.75 % Favored : 64.68 % 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: -3.88 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS A 31 PHE 0.029 0.002 PHE D 33 TYR 0.019 0.002 TYR E 114 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 67 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7539 (tmm) REVERT: A 103 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7880 (mtt180) REVERT: B 13 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7511 (tmm) REVERT: B 99 ASP cc_start: 0.7240 (t0) cc_final: 0.6448 (t0) REVERT: B 103 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6696 (mtt90) REVERT: D 13 MET cc_start: 0.8358 (ttm) cc_final: 0.8048 (tmm) REVERT: D 103 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7770 (mtt180) REVERT: E 62 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: E 74 ASP cc_start: 0.8255 (t70) cc_final: 0.7718 (t70) REVERT: E 95 PHE cc_start: 0.8768 (t80) cc_final: 0.8471 (t80) REVERT: E 103 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.5941 (mmp-170) outliers start: 33 outliers final: 24 residues processed: 88 average time/residue: 0.1579 time to fit residues: 16.9975 Evaluate side-chains 97 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3610 Z= 0.381 Angle : 0.693 8.719 4920 Z= 0.367 Chirality : 0.052 0.147 585 Planarity : 0.004 0.025 605 Dihedral : 5.635 20.108 485 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 9.35 % Allowed : 25.97 % Favored : 64.68 % 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: -3.83 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS A 31 PHE 0.025 0.002 PHE D 33 TYR 0.018 0.002 TYR E 114 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 70 time to evaluate : 0.466 Fit side-chains REVERT: A 13 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7547 (tmm) REVERT: A 103 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: B 13 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: B 99 ASP cc_start: 0.7376 (t0) cc_final: 0.6498 (t0) REVERT: B 103 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6864 (mtt90) REVERT: C 95 PHE cc_start: 0.8872 (t80) cc_final: 0.8559 (t80) REVERT: D 13 MET cc_start: 0.8359 (ttm) cc_final: 0.8047 (tmm) REVERT: D 103 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7862 (mtt180) REVERT: E 74 ASP cc_start: 0.8254 (t70) cc_final: 0.7784 (t70) REVERT: E 95 PHE cc_start: 0.8750 (t80) cc_final: 0.8383 (t80) REVERT: E 103 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.5951 (mmp-170) outliers start: 36 outliers final: 25 residues processed: 94 average time/residue: 0.1797 time to fit residues: 20.3355 Evaluate side-chains 97 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3610 Z= 0.198 Angle : 0.652 8.865 4920 Z= 0.337 Chirality : 0.052 0.139 585 Planarity : 0.004 0.023 605 Dihedral : 5.369 18.825 485 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 6.75 % Allowed : 27.53 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 79 HIS 0.001 0.000 HIS E 31 PHE 0.019 0.002 PHE B 33 TYR 0.022 0.001 TYR A 114 ARG 0.006 0.001 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 0.442 Fit side-chains REVERT: A 13 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7283 (tmm) REVERT: A 103 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7647 (mtt90) REVERT: B 100 SER cc_start: 0.8204 (p) cc_final: 0.7845 (m) REVERT: B 103 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6603 (mtt90) REVERT: C 95 PHE cc_start: 0.8816 (t80) cc_final: 0.8609 (t80) REVERT: D 13 MET cc_start: 0.8280 (ttm) cc_final: 0.8024 (tmm) REVERT: D 103 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (mtm-85) REVERT: E 62 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: E 103 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.5818 (mmp-170) outliers start: 26 outliers final: 15 residues processed: 93 average time/residue: 0.1678 time to fit residues: 18.9289 Evaluate side-chains 89 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.134246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.115743 restraints weight = 6056.511| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 3.01 r_work: 0.4220 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3610 Z= 0.294 Angle : 0.705 8.872 4920 Z= 0.364 Chirality : 0.052 0.167 585 Planarity : 0.003 0.025 605 Dihedral : 5.426 18.680 485 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.97 % Allowed : 28.83 % Favored : 65.19 % 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: -3.67 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 79 HIS 0.003 0.001 HIS A 31 PHE 0.021 0.002 PHE D 33 TYR 0.026 0.002 TYR A 114 ARG 0.003 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.18 seconds wall clock time: 22 minutes 33.28 seconds (1353.28 seconds total)