Starting phenix.real_space_refine on Thu Jan 18 00:47:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8d_18999/01_2024/8r8d_18999.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 38 5.16 5 C 4452 2.51 5 N 1192 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7062 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1664 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 798 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 798 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1664 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 4.43, per 1000 atoms: 0.63 Number of scatterers: 7062 At special positions: 0 Unit cell: (128.115, 84.315, 86.505, 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 38 16.00 O 1380 8.00 N 1192 7.00 C 4452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 6 " NAG-ASN " NAG C 1 " - " ASN B 74 " " NAG D 1 " - " ASN A 74 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 14 sheets defined 9.0% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.873A pdb=" N GLN B 60 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 60D through 63 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.823A pdb=" N ILE B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.593A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.795A pdb=" N GLU I 84 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.594A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.796A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.874A pdb=" N GLN A 60 " --> pdb=" O HIS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 60D through 63 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.823A pdb=" N ILE A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 242 Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 21 removed outlier: 3.661A pdb=" N ALA B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 199 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 229 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 182 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.549A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 87 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7 removed outlier: 5.887A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.807A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.300A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.009A pdb=" N ASP I 93 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.887A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.805A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.300A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 4.011A pdb=" N ASP L 93 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.661A pdb=" N ALA A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 199 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 229 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 182 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.550A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 87 " --> pdb=" O ARG A 107 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 582 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: 1.95 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2258 1.34 - 1.46: 1767 1.46 - 1.58: 3149 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 7218 Sorted by residual: bond pdb=" C5 FUC C 6 " pdb=" O5 FUC C 6 " ideal model delta sigma weight residual 1.423 1.458 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C5 FUC D 6 " pdb=" O5 FUC D 6 " ideal model delta sigma weight residual 1.423 1.458 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C5 MAN D 5 " pdb=" O5 MAN D 5 " ideal model delta sigma weight residual 1.418 1.445 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 MAN C 5 " pdb=" O5 MAN C 5 " ideal model delta sigma weight residual 1.418 1.445 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 MAN C 5 " pdb=" C2 MAN C 5 " ideal model delta sigma weight residual 1.526 1.552 -0.026 2.00e-02 2.50e+03 1.64e+00 ... (remaining 7213 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.39: 337 107.39 - 114.05: 3975 114.05 - 120.70: 2633 120.70 - 127.36: 2786 127.36 - 134.01: 107 Bond angle restraints: 9838 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C SER I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N ARG H 67 " pdb=" CA ARG H 67 " pdb=" C ARG H 67 " ideal model delta sigma weight residual 114.04 111.26 2.78 1.24e+00 6.50e-01 5.03e+00 angle pdb=" N ARG E 67 " pdb=" CA ARG E 67 " pdb=" C ARG E 67 " ideal model delta sigma weight residual 114.04 111.29 2.75 1.24e+00 6.50e-01 4.93e+00 angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.46e+00 ... (remaining 9833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 4054 21.36 - 42.72: 183 42.72 - 64.08: 35 64.08 - 85.44: 30 85.44 - 106.80: 8 Dihedral angle restraints: 4310 sinusoidal: 1710 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS A 168 " pdb=" SG CYS A 168 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS B 168 " pdb=" SG CYS B 168 " pdb=" SG CYS B 182 " pdb=" CB CYS B 182 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual 93.00 150.14 -57.14 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 4307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 917 0.057 - 0.114: 171 0.114 - 0.170: 30 0.170 - 0.227: 0 0.227 - 0.284: 2 Chirality restraints: 1120 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1117 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 48 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 49 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 48 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 49 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 115 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 116 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.025 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1068 2.77 - 3.30: 6362 3.30 - 3.83: 12223 3.83 - 4.37: 15300 4.37 - 4.90: 25681 Nonbonded interactions: 60634 Sorted by model distance: nonbonded pdb=" O PRO A 60C" pdb=" OH TYR A 88 " model vdw 2.232 2.440 nonbonded pdb=" O PRO B 60C" pdb=" OH TYR B 88 " model vdw 2.232 2.440 nonbonded pdb=" O PRO E 41 " pdb=" NZ LYS E 43 " model vdw 2.256 2.520 nonbonded pdb=" O PRO H 41 " pdb=" NZ LYS H 43 " model vdw 2.256 2.520 nonbonded pdb=" O ARG A 24 " pdb=" NH1 ARG A 24 " model vdw 2.287 2.520 ... (remaining 60629 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } 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: 1.520 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: 0.000 Extract box with map and model: 5.020 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.600 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7218 Z= 0.226 Angle : 0.666 8.596 9838 Z= 0.314 Chirality : 0.047 0.284 1120 Planarity : 0.005 0.059 1248 Dihedral : 14.826 106.800 2622 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.28), residues: 900 helix: -1.32 (0.75), residues: 42 sheet: 0.41 (0.34), residues: 252 loop : 0.10 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS A 27 PHE 0.011 0.001 PHE E 29 TYR 0.026 0.002 TYR E 112 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.8124 (tt0) cc_final: 0.7478 (tp30) REVERT: I 83 ASP cc_start: 0.8661 (m-30) cc_final: 0.8346 (m-30) REVERT: L 83 ASP cc_start: 0.8676 (m-30) cc_final: 0.8364 (m-30) REVERT: A 71 GLU cc_start: 0.8131 (tt0) cc_final: 0.7473 (tp30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 1.2437 time to fit residues: 182.9449 Evaluate side-chains 120 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN E 82 GLN I 54 GLN H 82 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7218 Z= 0.234 Angle : 0.653 9.485 9838 Z= 0.321 Chirality : 0.046 0.149 1120 Planarity : 0.005 0.039 1248 Dihedral : 8.291 60.173 1158 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.03 % Allowed : 5.92 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 900 helix: -1.12 (0.79), residues: 42 sheet: 0.52 (0.32), residues: 252 loop : 0.17 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS B 241 PHE 0.012 0.001 PHE H 29 TYR 0.019 0.002 TYR E 112 ARG 0.006 0.001 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.8285 (tt0) cc_final: 0.7198 (tp30) REVERT: A 71 GLU cc_start: 0.8281 (tt0) cc_final: 0.7150 (tp30) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 1.2570 time to fit residues: 174.5397 Evaluate side-chains 136 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7218 Z= 0.272 Angle : 0.662 9.163 9838 Z= 0.324 Chirality : 0.047 0.169 1120 Planarity : 0.005 0.038 1248 Dihedral : 7.227 47.641 1158 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.20 % Allowed : 9.09 % Favored : 88.71 % 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: 0.27 (0.28), residues: 900 helix: -1.15 (0.78), residues: 42 sheet: 0.63 (0.32), residues: 252 loop : 0.16 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 141 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.002 PHE E 29 TYR 0.012 0.002 TYR E 80 ARG 0.005 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.830 Fit side-chains REVERT: E 98 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8601 (ptt180) REVERT: H 98 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8595 (ptt180) outliers start: 16 outliers final: 14 residues processed: 130 average time/residue: 1.2581 time to fit residues: 171.9305 Evaluate side-chains 133 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7218 Z= 0.293 Angle : 0.678 8.654 9838 Z= 0.331 Chirality : 0.048 0.170 1120 Planarity : 0.005 0.039 1248 Dihedral : 6.551 36.572 1158 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.20 % Allowed : 11.29 % Favored : 86.50 % 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: 0.21 (0.28), residues: 900 helix: -1.21 (0.76), residues: 42 sheet: 0.64 (0.32), residues: 252 loop : 0.09 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS B 241 PHE 0.013 0.002 PHE E 29 TYR 0.012 0.002 TYR B 117 ARG 0.005 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.770 Fit side-chains REVERT: E 98 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8621 (ptt180) REVERT: H 98 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8614 (ptt180) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 1.2868 time to fit residues: 171.6496 Evaluate side-chains 131 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7218 Z= 0.222 Angle : 0.625 9.143 9838 Z= 0.305 Chirality : 0.046 0.155 1120 Planarity : 0.005 0.038 1248 Dihedral : 6.018 31.615 1158 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.20 % Allowed : 11.85 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 900 helix: -1.07 (0.78), residues: 42 sheet: 0.68 (0.31), residues: 272 loop : 0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS B 57 PHE 0.013 0.001 PHE E 29 TYR 0.012 0.002 TYR H 80 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.816 Fit side-chains REVERT: E 98 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8626 (ptt180) REVERT: H 98 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8622 (ptt180) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 1.3360 time to fit residues: 182.1915 Evaluate side-chains 132 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7218 Z= 0.234 Angle : 0.629 9.184 9838 Z= 0.308 Chirality : 0.045 0.149 1120 Planarity : 0.005 0.039 1248 Dihedral : 5.849 29.868 1158 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.62 % Allowed : 11.71 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 900 helix: -1.09 (0.77), residues: 42 sheet: 0.66 (0.31), residues: 272 loop : 0.10 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS A 57 PHE 0.013 0.002 PHE H 29 TYR 0.011 0.002 TYR B 117 ARG 0.008 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.755 Fit side-chains REVERT: E 98 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8622 (ptt180) REVERT: H 98 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8617 (ptt180) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 1.2904 time to fit residues: 169.2945 Evaluate side-chains 133 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7218 Z= 0.261 Angle : 0.645 8.967 9838 Z= 0.316 Chirality : 0.046 0.149 1120 Planarity : 0.005 0.038 1248 Dihedral : 5.797 28.446 1158 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.62 % Allowed : 12.26 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 900 helix: -1.12 (0.77), residues: 42 sheet: 0.67 (0.31), residues: 272 loop : 0.08 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 141 HIS 0.004 0.001 HIS B 241 PHE 0.013 0.002 PHE H 29 TYR 0.012 0.002 TYR E 80 ARG 0.008 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.730 Fit side-chains REVERT: E 98 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8622 (ptt180) REVERT: H 98 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8618 (ptt180) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 1.3741 time to fit residues: 183.1238 Evaluate side-chains 130 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN I 39 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7218 Z= 0.289 Angle : 0.670 8.625 9838 Z= 0.328 Chirality : 0.047 0.199 1120 Planarity : 0.005 0.037 1248 Dihedral : 5.810 26.982 1158 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.44 % Allowed : 11.98 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 900 helix: -1.16 (0.76), residues: 42 sheet: 0.68 (0.32), residues: 252 loop : 0.08 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 141 HIS 0.004 0.001 HIS B 27 PHE 0.014 0.002 PHE H 29 TYR 0.014 0.002 TYR A 117 ARG 0.007 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.748 Fit side-chains REVERT: E 98 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8629 (ptt180) REVERT: H 98 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8625 (ptt180) outliers start: 25 outliers final: 17 residues processed: 135 average time/residue: 1.2715 time to fit residues: 180.6051 Evaluate side-chains 137 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 GLN L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7218 Z= 0.206 Angle : 0.611 9.511 9838 Z= 0.300 Chirality : 0.045 0.154 1120 Planarity : 0.005 0.038 1248 Dihedral : 5.529 25.082 1158 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.03 % Allowed : 12.53 % Favored : 84.44 % 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: 0.39 (0.28), residues: 900 helix: 0.65 (0.96), residues: 30 sheet: 0.74 (0.31), residues: 272 loop : 0.08 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS B 57 PHE 0.013 0.001 PHE E 29 TYR 0.012 0.002 TYR H 80 ARG 0.007 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.784 Fit side-chains REVERT: E 98 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8624 (ptt180) REVERT: H 98 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8619 (ptt180) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 1.2439 time to fit residues: 175.9050 Evaluate side-chains 136 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN I 39 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7218 Z= 0.223 Angle : 0.627 9.090 9838 Z= 0.308 Chirality : 0.045 0.152 1120 Planarity : 0.005 0.041 1248 Dihedral : 5.468 24.142 1158 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.44 % Allowed : 12.67 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 900 helix: -1.02 (0.78), residues: 42 sheet: 0.72 (0.31), residues: 272 loop : 0.16 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.005 0.001 HIS B 57 PHE 0.014 0.001 PHE H 29 TYR 0.019 0.002 TYR E 112 ARG 0.007 0.001 ARG B 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.828 Fit side-chains REVERT: B 157 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7603 (pt0) REVERT: E 98 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8623 (ptt180) REVERT: H 98 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8619 (ptt180) REVERT: A 157 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7600 (pt0) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 1.2399 time to fit residues: 173.3733 Evaluate side-chains 143 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124370 restraints weight = 6866.666| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.53 r_work: 0.3321 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 7218 Z= 0.275 Angle : 1.020 61.599 9838 Z= 0.479 Chirality : 0.047 0.271 1120 Planarity : 0.005 0.042 1248 Dihedral : 5.496 24.096 1158 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.31 % Allowed : 12.40 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 900 helix: -1.03 (0.78), residues: 42 sheet: 0.70 (0.30), residues: 272 loop : 0.16 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS B 57 PHE 0.014 0.002 PHE H 29 TYR 0.016 0.002 TYR E 112 ARG 0.006 0.001 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.83 seconds wall clock time: 57 minutes 48.78 seconds (3468.78 seconds total)