Starting phenix.real_space_refine on Sat Jul 20 10:07:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqg_33395/07_2024/7xqg_33395.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 48 5.16 5 C 6846 2.51 5 N 1566 2.21 5 O 1740 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-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 6.12, per 1000 atoms: 0.60 Number of scatterers: 10206 At special positions: 0 Unit cell: (106, 111.088, 99.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 6 15.00 O 1740 8.00 N 1566 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 177 Processing helix chain 'A' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 177 Processing helix chain 'B' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 177 Processing helix chain 'C' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.602A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 177 Processing helix chain 'D' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.534A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.795A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 177 Processing helix chain 'E' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.511A pdb=" N GLN F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 177 Processing helix chain 'F' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2088 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: 2.92 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1597 1.33 - 1.45: 2897 1.45 - 1.57: 5910 1.57 - 1.69: 12 1.69 - 1.81: 60 Bond restraints: 10476 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.95e-01 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.90e-01 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.82e-01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 92.58 - 100.86: 18 100.86 - 109.14: 518 109.14 - 117.42: 7128 117.42 - 125.70: 6339 125.70 - 133.98: 187 Bond angle restraints: 14190 Sorted by residual: angle pdb=" C SER C 201 " pdb=" N ARG C 202 " pdb=" CA ARG C 202 " ideal model delta sigma weight residual 121.80 127.27 -5.47 2.44e+00 1.68e-01 5.02e+00 angle pdb=" C SER F 201 " pdb=" N ARG F 202 " pdb=" CA ARG F 202 " ideal model delta sigma weight residual 121.80 127.26 -5.46 2.44e+00 1.68e-01 5.01e+00 angle pdb=" C SER E 201 " pdb=" N ARG E 202 " pdb=" CA ARG E 202 " ideal model delta sigma weight residual 121.80 127.25 -5.45 2.44e+00 1.68e-01 4.99e+00 angle pdb=" C SER A 201 " pdb=" N ARG A 202 " pdb=" CA ARG A 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 angle pdb=" C SER D 201 " pdb=" N ARG D 202 " pdb=" CA ARG D 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 ... (remaining 14185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 6026 16.74 - 33.48: 303 33.48 - 50.22: 97 50.22 - 66.97: 24 66.97 - 83.71: 12 Dihedral angle restraints: 6462 sinusoidal: 2934 harmonic: 3528 Sorted by residual: dihedral pdb=" N PHE A 212 " pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sinusoidal sigma weight residual 180.00 -126.50 -53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE C 212 " pdb=" CA PHE C 212 " pdb=" CB PHE C 212 " pdb=" CG PHE C 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.52 -53.48 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE B 212 " pdb=" CA PHE B 212 " pdb=" CB PHE B 212 " pdb=" CG PHE B 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.53 -53.47 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 6459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 878 0.021 - 0.041: 409 0.041 - 0.062: 227 0.062 - 0.083: 53 0.083 - 0.103: 35 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.66e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 chirality pdb=" CA VAL C 184 " pdb=" N VAL C 184 " pdb=" C VAL C 184 " pdb=" CB VAL C 184 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 1599 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 190 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO E 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO E 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 191 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 190 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO C 191 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 190 " 0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO F 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.011 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2430 2.79 - 3.32: 10217 3.32 - 3.85: 16371 3.85 - 4.37: 16449 4.37 - 4.90: 30061 Nonbonded interactions: 75528 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG1 THR C 39 " model vdw 2.268 2.440 nonbonded pdb=" O LEU F 35 " pdb=" OG1 THR F 39 " model vdw 2.268 2.440 nonbonded pdb=" O LEU D 35 " pdb=" OG1 THR D 39 " model vdw 2.268 2.440 nonbonded pdb=" O LEU A 35 " pdb=" OG1 THR A 39 " model vdw 2.268 2.440 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.268 2.440 ... (remaining 75523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.080 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.690 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.002 0.018 10476 Z= 0.123 Angle : 0.459 6.101 14190 Z= 0.234 Chirality : 0.032 0.103 1602 Planarity : 0.002 0.021 1674 Dihedral : 12.111 83.707 4128 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.52 % Favored : 97.97 % Rotamer: Outliers : 5.00 % Allowed : 3.89 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.24), residues: 1182 helix: 2.75 (0.17), residues: 834 sheet: 3.07 (0.70), residues: 66 loop : -0.84 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 78 HIS 0.001 0.000 HIS F 194 PHE 0.006 0.001 PHE E 32 TYR 0.008 0.001 TYR C 155 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 296 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8362 (p0) cc_final: 0.8146 (p0) REVERT: A 173 GLN cc_start: 0.9564 (tt0) cc_final: 0.8945 (tm-30) REVERT: B 47 ASP cc_start: 0.8326 (p0) cc_final: 0.8049 (p0) REVERT: B 92 TYR cc_start: 0.9254 (t80) cc_final: 0.9052 (t80) REVERT: B 103 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9290 (mm-30) REVERT: B 173 GLN cc_start: 0.9582 (tt0) cc_final: 0.8986 (tm-30) REVERT: C 47 ASP cc_start: 0.8056 (p0) cc_final: 0.7758 (p0) REVERT: C 92 TYR cc_start: 0.9307 (t80) cc_final: 0.9097 (t80) REVERT: C 173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9013 (tm-30) REVERT: D 47 ASP cc_start: 0.8142 (p0) cc_final: 0.7864 (p0) REVERT: D 103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9096 (tp30) REVERT: E 47 ASP cc_start: 0.8197 (p0) cc_final: 0.7835 (p0) REVERT: E 101 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8595 (tpt170) REVERT: E 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.8998 (tm-30) REVERT: F 47 ASP cc_start: 0.8159 (p0) cc_final: 0.7887 (p0) REVERT: F 101 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8688 (tpt170) REVERT: F 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9032 (tm-30) REVERT: F 202 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8540 (ptp90) outliers start: 54 outliers final: 19 residues processed: 340 average time/residue: 0.2581 time to fit residues: 116.3078 Evaluate side-chains 205 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.0270 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10476 Z= 0.239 Angle : 0.689 9.900 14190 Z= 0.343 Chirality : 0.040 0.270 1602 Planarity : 0.003 0.026 1674 Dihedral : 11.505 85.836 1884 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.21 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 12.69 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.24), residues: 1182 helix: 2.63 (0.17), residues: 828 sheet: 2.37 (0.70), residues: 66 loop : -0.97 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 25 HIS 0.001 0.000 HIS F 74 PHE 0.008 0.001 PHE E 97 TYR 0.010 0.001 TYR D 66 ARG 0.006 0.001 ARG E 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8333 (p0) cc_final: 0.7954 (p0) REVERT: A 173 GLN cc_start: 0.9581 (tt0) cc_final: 0.8988 (tm-30) REVERT: B 53 ARG cc_start: 0.8822 (ptp-110) cc_final: 0.8618 (mtm110) REVERT: B 92 TYR cc_start: 0.9261 (t80) cc_final: 0.8685 (t80) REVERT: B 173 GLN cc_start: 0.9584 (tt0) cc_final: 0.8989 (tm-30) REVERT: C 92 TYR cc_start: 0.9320 (t80) cc_final: 0.8626 (t80) REVERT: C 173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9011 (tm-30) REVERT: D 103 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9154 (tp30) REVERT: D 155 TYR cc_start: 0.8244 (t80) cc_final: 0.7841 (t80) REVERT: D 173 GLN cc_start: 0.9629 (tt0) cc_final: 0.9074 (tm-30) REVERT: E 48 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: E 49 GLN cc_start: 0.8850 (tt0) cc_final: 0.8589 (mt0) REVERT: E 101 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8617 (tpt170) REVERT: E 173 GLN cc_start: 0.9557 (tt0) cc_final: 0.9066 (tm-30) REVERT: F 101 ARG cc_start: 0.8978 (mtp85) cc_final: 0.8766 (tpt170) REVERT: F 173 GLN cc_start: 0.9553 (tt0) cc_final: 0.9006 (tm-30) outliers start: 50 outliers final: 35 residues processed: 225 average time/residue: 0.2211 time to fit residues: 69.4874 Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10476 Z= 0.219 Angle : 0.686 11.478 14190 Z= 0.344 Chirality : 0.039 0.246 1602 Planarity : 0.004 0.032 1674 Dihedral : 11.221 88.328 1884 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.45 % Favored : 97.04 % Rotamer: Outliers : 4.54 % Allowed : 14.35 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.24), residues: 1182 helix: 2.70 (0.17), residues: 828 sheet: 1.92 (0.72), residues: 66 loop : -1.17 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 45 HIS 0.001 0.000 HIS E 74 PHE 0.006 0.001 PHE D 32 TYR 0.009 0.001 TYR C 66 ARG 0.005 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9576 (tt0) cc_final: 0.8975 (tm-30) REVERT: A 205 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 53 ARG cc_start: 0.8848 (ptp-110) cc_final: 0.8647 (mtt90) REVERT: B 92 TYR cc_start: 0.9270 (t80) cc_final: 0.8691 (t80) REVERT: B 173 GLN cc_start: 0.9594 (tt0) cc_final: 0.9059 (tm-30) REVERT: C 92 TYR cc_start: 0.9331 (t80) cc_final: 0.8632 (t80) REVERT: C 173 GLN cc_start: 0.9562 (tt0) cc_final: 0.9007 (tm-30) REVERT: D 47 ASP cc_start: 0.8113 (p0) cc_final: 0.7859 (p0) REVERT: D 103 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9207 (tp30) REVERT: D 155 TYR cc_start: 0.8409 (t80) cc_final: 0.7976 (t80) REVERT: E 101 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8636 (tpt170) REVERT: E 173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9071 (tm-30) REVERT: F 101 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8744 (tpt170) REVERT: F 173 GLN cc_start: 0.9554 (tt0) cc_final: 0.9003 (tm-30) REVERT: F 205 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8273 (mt-10) outliers start: 49 outliers final: 35 residues processed: 220 average time/residue: 0.2057 time to fit residues: 64.7933 Evaluate side-chains 198 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10476 Z= 0.196 Angle : 0.695 12.206 14190 Z= 0.347 Chirality : 0.038 0.227 1602 Planarity : 0.004 0.042 1674 Dihedral : 10.977 89.984 1884 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.05 % Favored : 96.45 % Rotamer: Outliers : 4.44 % Allowed : 15.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1182 helix: 2.66 (0.17), residues: 828 sheet: 1.47 (0.71), residues: 66 loop : -1.42 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 45 HIS 0.005 0.001 HIS F 194 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR B 66 ARG 0.006 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9202 (tp30) REVERT: A 173 GLN cc_start: 0.9548 (tt0) cc_final: 0.8980 (tm-30) REVERT: A 205 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 42 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 92 TYR cc_start: 0.9260 (t80) cc_final: 0.8663 (t80) REVERT: B 173 GLN cc_start: 0.9572 (tt0) cc_final: 0.9062 (tm-30) REVERT: C 92 TYR cc_start: 0.9316 (t80) cc_final: 0.8611 (t80) REVERT: C 173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9016 (tm-30) REVERT: D 47 ASP cc_start: 0.8088 (p0) cc_final: 0.7832 (p0) REVERT: D 92 TYR cc_start: 0.9459 (t80) cc_final: 0.9190 (t80) REVERT: D 103 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9188 (tp30) REVERT: D 155 TYR cc_start: 0.8399 (t80) cc_final: 0.8054 (t80) REVERT: E 47 ASP cc_start: 0.7886 (p0) cc_final: 0.7671 (p0) REVERT: E 61 CYS cc_start: 0.6290 (t) cc_final: 0.5911 (t) REVERT: E 101 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8696 (tpt170) REVERT: E 173 GLN cc_start: 0.9537 (tt0) cc_final: 0.9068 (tm-30) REVERT: F 61 CYS cc_start: 0.6346 (t) cc_final: 0.5362 (t) REVERT: F 62 GLU cc_start: 0.8873 (mp0) cc_final: 0.8188 (mm-30) REVERT: F 173 GLN cc_start: 0.9523 (tt0) cc_final: 0.9012 (tm-30) outliers start: 48 outliers final: 36 residues processed: 225 average time/residue: 0.2106 time to fit residues: 67.6323 Evaluate side-chains 197 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10476 Z= 0.204 Angle : 0.701 12.623 14190 Z= 0.347 Chirality : 0.039 0.235 1602 Planarity : 0.004 0.044 1674 Dihedral : 10.756 86.938 1884 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.45 % Favored : 97.04 % Rotamer: Outliers : 4.54 % Allowed : 16.85 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.24), residues: 1182 helix: 2.56 (0.17), residues: 852 sheet: 1.34 (0.71), residues: 66 loop : -1.23 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.000 TRP F 45 HIS 0.004 0.000 HIS C 194 PHE 0.007 0.001 PHE A 32 TYR 0.009 0.001 TYR B 66 ARG 0.007 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9213 (tp30) REVERT: A 173 GLN cc_start: 0.9531 (tt0) cc_final: 0.9001 (tm-30) REVERT: B 92 TYR cc_start: 0.9303 (t80) cc_final: 0.8699 (t80) REVERT: B 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9069 (tm-30) REVERT: B 205 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8487 (mt-10) REVERT: C 92 TYR cc_start: 0.9343 (t80) cc_final: 0.8676 (t80) REVERT: C 173 GLN cc_start: 0.9528 (tt0) cc_final: 0.9031 (tm-30) REVERT: D 47 ASP cc_start: 0.8121 (p0) cc_final: 0.7876 (p0) REVERT: D 92 TYR cc_start: 0.9453 (t80) cc_final: 0.9202 (t80) REVERT: D 155 TYR cc_start: 0.8464 (t80) cc_final: 0.8151 (t80) REVERT: D 173 GLN cc_start: 0.9581 (tt0) cc_final: 0.9118 (tm-30) REVERT: E 101 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8737 (tpt170) REVERT: E 173 GLN cc_start: 0.9530 (tt0) cc_final: 0.9107 (tm-30) REVERT: F 173 GLN cc_start: 0.9539 (tt0) cc_final: 0.9040 (tm-30) REVERT: F 205 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8373 (mt-10) outliers start: 49 outliers final: 39 residues processed: 212 average time/residue: 0.1962 time to fit residues: 59.9644 Evaluate side-chains 204 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10476 Z= 0.189 Angle : 0.704 11.664 14190 Z= 0.347 Chirality : 0.038 0.210 1602 Planarity : 0.004 0.039 1674 Dihedral : 10.508 86.042 1884 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.13 % Favored : 96.45 % Rotamer: Outliers : 4.07 % Allowed : 17.87 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.24), residues: 1182 helix: 2.54 (0.17), residues: 852 sheet: 1.04 (0.72), residues: 66 loop : -1.16 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP F 45 HIS 0.001 0.000 HIS B 194 PHE 0.008 0.001 PHE A 32 TYR 0.007 0.001 TYR A 155 ARG 0.008 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9518 (tt0) cc_final: 0.9021 (tm-30) REVERT: B 92 TYR cc_start: 0.9309 (t80) cc_final: 0.8678 (t80) REVERT: B 173 GLN cc_start: 0.9551 (tt0) cc_final: 0.9073 (tm-30) REVERT: C 62 GLU cc_start: 0.8744 (mp0) cc_final: 0.8361 (mp0) REVERT: C 92 TYR cc_start: 0.9340 (t80) cc_final: 0.8678 (t80) REVERT: C 173 GLN cc_start: 0.9512 (tt0) cc_final: 0.9054 (tm-30) REVERT: C 195 GLN cc_start: 0.9171 (mt0) cc_final: 0.8692 (pp30) REVERT: D 47 ASP cc_start: 0.8125 (p0) cc_final: 0.7869 (p0) REVERT: D 92 TYR cc_start: 0.9446 (t80) cc_final: 0.9207 (t80) REVERT: D 155 TYR cc_start: 0.8483 (t80) cc_final: 0.8168 (t80) REVERT: D 173 GLN cc_start: 0.9558 (tt0) cc_final: 0.9112 (tm-30) REVERT: D 195 GLN cc_start: 0.9177 (mt0) cc_final: 0.8600 (pp30) REVERT: E 101 ARG cc_start: 0.8989 (mtp85) cc_final: 0.8786 (tpt170) REVERT: E 173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9112 (tm-30) REVERT: F 173 GLN cc_start: 0.9516 (tt0) cc_final: 0.9030 (tm-30) REVERT: F 205 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8467 (mt-10) outliers start: 44 outliers final: 39 residues processed: 214 average time/residue: 0.1996 time to fit residues: 61.1666 Evaluate side-chains 204 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10476 Z= 0.210 Angle : 0.706 11.222 14190 Z= 0.348 Chirality : 0.038 0.191 1602 Planarity : 0.004 0.047 1674 Dihedral : 10.348 86.694 1882 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.17 % Allowed : 17.69 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1182 helix: 2.54 (0.17), residues: 852 sheet: 1.63 (0.71), residues: 60 loop : -1.33 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP F 45 HIS 0.001 0.000 HIS D 194 PHE 0.007 0.001 PHE F 32 TYR 0.007 0.001 TYR A 155 ARG 0.007 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9542 (tt0) cc_final: 0.9071 (tm-30) REVERT: A 195 GLN cc_start: 0.9215 (mt0) cc_final: 0.8592 (pp30) REVERT: B 42 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 92 TYR cc_start: 0.9333 (t80) cc_final: 0.8721 (t80) REVERT: B 173 GLN cc_start: 0.9574 (tt0) cc_final: 0.9091 (tm-30) REVERT: B 205 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8573 (mp0) REVERT: C 92 TYR cc_start: 0.9355 (t80) cc_final: 0.8714 (t80) REVERT: C 173 GLN cc_start: 0.9524 (tt0) cc_final: 0.9031 (tm-30) REVERT: C 195 GLN cc_start: 0.9157 (mt0) cc_final: 0.8705 (pp30) REVERT: D 47 ASP cc_start: 0.8140 (p0) cc_final: 0.7883 (p0) REVERT: D 155 TYR cc_start: 0.8547 (t80) cc_final: 0.8181 (t80) REVERT: D 173 GLN cc_start: 0.9569 (tt0) cc_final: 0.9114 (tm-30) REVERT: D 195 GLN cc_start: 0.9197 (mt0) cc_final: 0.8541 (pp30) REVERT: E 101 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8689 (tpt170) REVERT: E 173 GLN cc_start: 0.9541 (tt0) cc_final: 0.9134 (tm-30) REVERT: E 205 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8469 (mt-10) REVERT: F 173 GLN cc_start: 0.9515 (tt0) cc_final: 0.9026 (tm-30) outliers start: 45 outliers final: 38 residues processed: 203 average time/residue: 0.2151 time to fit residues: 62.3106 Evaluate side-chains 201 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10476 Z= 0.184 Angle : 0.715 10.263 14190 Z= 0.353 Chirality : 0.038 0.192 1602 Planarity : 0.004 0.044 1674 Dihedral : 10.131 87.468 1880 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.07 % Allowed : 18.24 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.24), residues: 1182 helix: 2.51 (0.17), residues: 852 sheet: 1.65 (0.73), residues: 60 loop : -1.39 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP F 45 HIS 0.001 0.000 HIS D 194 PHE 0.008 0.001 PHE F 32 TYR 0.007 0.001 TYR A 155 ARG 0.008 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9524 (tt0) cc_final: 0.9075 (tm-30) REVERT: A 195 GLN cc_start: 0.9208 (mt0) cc_final: 0.8600 (pp30) REVERT: B 92 TYR cc_start: 0.9297 (t80) cc_final: 0.8739 (t80) REVERT: B 173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9089 (tm-30) REVERT: B 195 GLN cc_start: 0.9120 (mt0) cc_final: 0.8526 (pp30) REVERT: C 92 TYR cc_start: 0.9314 (t80) cc_final: 0.8787 (t80) REVERT: C 173 GLN cc_start: 0.9517 (tt0) cc_final: 0.9082 (tm-30) REVERT: C 195 GLN cc_start: 0.9131 (mt0) cc_final: 0.8503 (pp30) REVERT: D 47 ASP cc_start: 0.8133 (p0) cc_final: 0.7878 (p0) REVERT: D 155 TYR cc_start: 0.8533 (t80) cc_final: 0.8174 (t80) REVERT: D 173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9131 (tm-30) REVERT: D 195 GLN cc_start: 0.9192 (mt0) cc_final: 0.8516 (pp30) REVERT: E 101 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8669 (tpt170) REVERT: E 173 GLN cc_start: 0.9520 (tt0) cc_final: 0.9137 (tm-30) REVERT: E 205 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8433 (mt-10) REVERT: F 92 TYR cc_start: 0.9194 (t80) cc_final: 0.8790 (t80) REVERT: F 173 GLN cc_start: 0.9506 (tt0) cc_final: 0.9038 (tm-30) REVERT: F 195 GLN cc_start: 0.9141 (mt0) cc_final: 0.8743 (pp30) outliers start: 44 outliers final: 36 residues processed: 212 average time/residue: 0.2068 time to fit residues: 62.3029 Evaluate side-chains 198 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.0070 chunk 33 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10476 Z= 0.186 Angle : 0.734 10.068 14190 Z= 0.359 Chirality : 0.038 0.179 1602 Planarity : 0.004 0.053 1674 Dihedral : 9.997 88.007 1880 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 19.17 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.24), residues: 1182 helix: 2.49 (0.17), residues: 852 sheet: 1.58 (0.73), residues: 60 loop : -1.43 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP F 45 HIS 0.001 0.000 HIS D 194 PHE 0.008 0.001 PHE A 32 TYR 0.006 0.001 TYR A 155 ARG 0.014 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9080 (tm-30) REVERT: A 195 GLN cc_start: 0.9188 (mt0) cc_final: 0.8601 (pp30) REVERT: B 92 TYR cc_start: 0.9299 (t80) cc_final: 0.8708 (t80) REVERT: B 173 GLN cc_start: 0.9524 (tt0) cc_final: 0.9082 (tm-30) REVERT: B 195 GLN cc_start: 0.9111 (mt0) cc_final: 0.8548 (pp30) REVERT: C 92 TYR cc_start: 0.9306 (t80) cc_final: 0.8800 (t80) REVERT: C 173 GLN cc_start: 0.9497 (tt0) cc_final: 0.9081 (tm-30) REVERT: C 195 GLN cc_start: 0.9064 (mt0) cc_final: 0.8540 (pp30) REVERT: D 47 ASP cc_start: 0.8151 (p0) cc_final: 0.7893 (p0) REVERT: D 92 TYR cc_start: 0.9448 (t80) cc_final: 0.9228 (t80) REVERT: D 155 TYR cc_start: 0.8518 (t80) cc_final: 0.8219 (t80) REVERT: D 173 GLN cc_start: 0.9532 (tt0) cc_final: 0.9140 (tm-30) REVERT: D 195 GLN cc_start: 0.9071 (mt0) cc_final: 0.8490 (pp30) REVERT: E 92 TYR cc_start: 0.9152 (t80) cc_final: 0.8798 (t80) REVERT: E 173 GLN cc_start: 0.9496 (tt0) cc_final: 0.9133 (tm-30) REVERT: E 195 GLN cc_start: 0.9141 (mt0) cc_final: 0.8750 (pp30) REVERT: F 92 TYR cc_start: 0.9200 (t80) cc_final: 0.8788 (t80) REVERT: F 173 GLN cc_start: 0.9484 (tt0) cc_final: 0.9035 (tm-30) REVERT: F 195 GLN cc_start: 0.9133 (mt0) cc_final: 0.8793 (pp30) outliers start: 37 outliers final: 35 residues processed: 209 average time/residue: 0.2069 time to fit residues: 62.0777 Evaluate side-chains 199 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10476 Z= 0.236 Angle : 0.730 9.981 14190 Z= 0.364 Chirality : 0.039 0.188 1602 Planarity : 0.004 0.044 1674 Dihedral : 9.976 88.992 1874 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.43 % Allowed : 19.63 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.24), residues: 1182 helix: 2.59 (0.17), residues: 846 sheet: 1.50 (0.72), residues: 60 loop : -1.51 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 45 HIS 0.002 0.000 HIS D 194 PHE 0.009 0.001 PHE F 209 TYR 0.008 0.001 TYR A 155 ARG 0.008 0.001 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9546 (tt0) cc_final: 0.9077 (tm-30) REVERT: A 195 GLN cc_start: 0.9174 (mt0) cc_final: 0.8627 (pp30) REVERT: B 92 TYR cc_start: 0.9338 (t80) cc_final: 0.8771 (t80) REVERT: B 173 GLN cc_start: 0.9582 (tt0) cc_final: 0.9110 (tm-30) REVERT: B 195 GLN cc_start: 0.9119 (mt0) cc_final: 0.8622 (pp30) REVERT: C 92 TYR cc_start: 0.9348 (t80) cc_final: 0.8815 (t80) REVERT: C 173 GLN cc_start: 0.9531 (tt0) cc_final: 0.9055 (tm-30) REVERT: C 195 GLN cc_start: 0.9068 (mt0) cc_final: 0.8577 (pp30) REVERT: D 47 ASP cc_start: 0.8154 (p0) cc_final: 0.7921 (p0) REVERT: D 155 TYR cc_start: 0.8642 (t80) cc_final: 0.8331 (t80) REVERT: D 173 GLN cc_start: 0.9574 (tt0) cc_final: 0.9124 (tm-30) REVERT: D 195 GLN cc_start: 0.9134 (mt0) cc_final: 0.8534 (pp30) REVERT: E 42 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8326 (tm-30) REVERT: E 92 TYR cc_start: 0.9208 (t80) cc_final: 0.8876 (t80) REVERT: E 173 GLN cc_start: 0.9545 (tt0) cc_final: 0.9129 (tm-30) REVERT: E 195 GLN cc_start: 0.9108 (mt0) cc_final: 0.8699 (pp30) REVERT: F 173 GLN cc_start: 0.9529 (tt0) cc_final: 0.9048 (tm-30) REVERT: F 195 GLN cc_start: 0.9115 (mt0) cc_final: 0.8818 (pp30) outliers start: 37 outliers final: 34 residues processed: 199 average time/residue: 0.2124 time to fit residues: 60.0161 Evaluate side-chains 196 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 107 ASN ** 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 = 0.3440 r_free = 0.3440 target = 0.073310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057981 restraints weight = 43073.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059881 restraints weight = 21966.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061255 restraints weight = 14185.018| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10476 Z= 0.187 Angle : 0.741 10.158 14190 Z= 0.360 Chirality : 0.037 0.175 1602 Planarity : 0.004 0.043 1674 Dihedral : 9.792 88.766 1872 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.15 % Allowed : 20.37 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.24), residues: 1182 helix: 2.57 (0.17), residues: 846 sheet: 1.39 (0.73), residues: 60 loop : -1.57 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP F 45 HIS 0.001 0.000 HIS E 194 PHE 0.008 0.001 PHE A 32 TYR 0.006 0.001 TYR D 66 ARG 0.008 0.001 ARG F 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.05 seconds wall clock time: 37 minutes 49.98 seconds (2269.98 seconds total)