Starting phenix.real_space_refine on Thu Jul 2 02:57:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwy_43605/07_2026/8vwy_43605.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.024 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 Ca 7 9.91 5 S 52 5.16 5 C 4047 2.51 5 N 1016 2.21 5 O 1171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6293 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "H" Number of atoms: 1036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1052 Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.72, per 1000 atoms: 0.27 Number of scatterers: 6293 At special positions: 0 Unit cell: (99.256, 104.48, 78.36, 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) Ca 7 19.99 S 52 16.00 O 1171 8.00 N 1016 7.00 C 4047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 29 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 29 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 29 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 163 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.44 Conformation dependent library (CDL) restraints added in 372.7 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.5% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 68 through 79 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 68 through 79 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 138 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.513A pdb=" N THR A 6 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 34 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 62 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 60 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 17 removed outlier: 3.563A pdb=" N GLY A 14 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 126 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 48 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 29 through 34 removed outlier: 5.106A pdb=" N VAL E 30 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY E 14 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE E 52 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.734A pdb=" N GLY E 116 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.599A pdb=" N LYS E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.599A pdb=" N LYS E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 34 removed outlier: 6.379A pdb=" N TYR H 12 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN H 33 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA H 10 " --> pdb=" O ASN H 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE H 52 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.557A pdb=" N LYS H 44 " --> pdb=" O ASP H 39 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU H 73 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.557A pdb=" N LYS H 44 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 29 through 34 removed outlier: 5.226A pdb=" N VAL I 30 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY I 14 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA I 10 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE I 52 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.552A pdb=" N LYS I 44 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU I 73 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.552A pdb=" N LYS I 44 " --> pdb=" O ASP I 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.539A pdb=" N THR B 6 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 34 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 62 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 60 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.660A pdb=" N GLY B 14 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B 126 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 43 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.535A pdb=" N THR C 6 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 34 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 62 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 60 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 17 removed outlier: 3.645A pdb=" N GLY C 14 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 126 " --> pdb=" O SER C 48 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.57 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: 1966 1.34 - 1.46: 1609 1.46 - 1.58: 2795 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6438 Sorted by residual: bond pdb=" C PHE E 132 " pdb=" N ILE E 133 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.46e-02 4.69e+03 2.83e+00 bond pdb=" CB VAL H 99 " pdb=" CG1 VAL H 99 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CB VAL E 99 " pdb=" CG1 VAL E 99 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB VAL I 99 " pdb=" CG1 VAL I 99 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C PHE I 132 " pdb=" N ILE I 133 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.96e-02 2.60e+03 1.36e+00 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8262 1.14 - 2.27: 405 2.27 - 3.41: 58 3.41 - 4.55: 20 4.55 - 5.68: 2 Bond angle restraints: 8747 Sorted by residual: angle pdb=" C ASN E 76 " pdb=" CA ASN E 76 " pdb=" CB ASN E 76 " ideal model delta sigma weight residual 110.42 115.45 -5.03 1.99e+00 2.53e-01 6.39e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 117.88 -3.98 1.80e+00 3.09e-01 4.89e+00 angle pdb=" CA TYR I 53 " pdb=" CB TYR I 53 " pdb=" CG TYR I 53 " ideal model delta sigma weight residual 113.90 117.70 -3.80 1.80e+00 3.09e-01 4.47e+00 angle pdb=" CA TYR H 53 " pdb=" CB TYR H 53 " pdb=" CG TYR H 53 " ideal model delta sigma weight residual 113.90 117.52 -3.62 1.80e+00 3.09e-01 4.04e+00 angle pdb=" N ASN E 76 " pdb=" CA ASN E 76 " pdb=" C ASN E 76 " ideal model delta sigma weight residual 110.80 106.58 4.22 2.13e+00 2.20e-01 3.92e+00 ... (remaining 8742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3435 16.43 - 32.85: 245 32.85 - 49.27: 64 49.27 - 65.70: 8 65.70 - 82.12: 3 Dihedral angle restraints: 3755 sinusoidal: 1345 harmonic: 2410 Sorted by residual: dihedral pdb=" CA ASP H 29 " pdb=" C ASP H 29 " pdb=" N VAL H 30 " pdb=" CA VAL H 30 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS C 99 " pdb=" C LYS C 99 " pdb=" N ASN C 100 " pdb=" CA ASN C 100 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ASP I 29 " pdb=" C ASP I 29 " pdb=" N VAL I 30 " pdb=" CA VAL I 30 " ideal model delta harmonic sigma weight residual -180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 3752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.053: 280 0.053 - 0.080: 95 0.080 - 0.106: 44 0.106 - 0.132: 29 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ILE I 49 " pdb=" N ILE I 49 " pdb=" C ILE I 49 " pdb=" CB ILE I 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE H 49 " pdb=" N ILE H 49 " pdb=" C ILE H 49 " pdb=" CB ILE H 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO H 40 " pdb=" N PRO H 40 " pdb=" C PRO H 40 " pdb=" CB PRO H 40 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 961 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 32 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C THR I 32 " -0.020 2.00e-02 2.50e+03 pdb=" O THR I 32 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN I 33 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 53 " -0.012 2.00e-02 2.50e+03 8.15e-03 1.33e+00 pdb=" CG TYR H 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " 0.012 2.00e-02 2.50e+03 7.97e-03 1.27e+00 pdb=" CG TYR E 53 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 185 2.69 - 3.24: 5793 3.24 - 3.79: 10529 3.79 - 4.35: 14023 4.35 - 4.90: 23755 Nonbonded interactions: 54285 Sorted by model distance: nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN A 103 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR C 62 " pdb=" OE1 GLN C 103 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN B 103 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASP H 39 " pdb=" OG1 THR H 41 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP I 39 " pdb=" OG1 THR I 41 " model vdw 2.215 3.040 ... (remaining 54280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 173) selection = (chain 'C' and resid 4 through 173) } ncs_group { reference = (chain 'E' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'H' and (resid 6 through 68 or resid 70 through 201)) selection = (chain 'I' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 201)) } 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=0.39 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.080 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.006 0.042 6453 Z= 0.291 Angle : 0.580 5.682 8777 Z= 0.323 Chirality : 0.042 0.132 964 Planarity : 0.003 0.021 1116 Dihedral : 12.577 82.124 2166 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.10 % Allowed : 10.33 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.28), residues: 802 helix: -0.16 (0.52), residues: 93 sheet: -0.60 (0.29), residues: 304 loop : -1.29 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 17 TYR 0.019 0.002 TYR H 53 PHE 0.007 0.002 PHE I 55 TRP 0.003 0.001 TRP B 31 HIS 0.003 0.001 HIS I 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 ( 6438) covalent geometry : angle 0.58000 / 0.32 ( 8747) SS BOND : bond 0.00123 / 0.08 ( 15) SS BOND : angle 0.44138 / 0.27 ( 30) hydrogen bonds : bond 0.24366 / 16.42 ( 250) hydrogen bonds : angle 9.76773 / 6.79 ( 731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7404 (m-30) cc_final: 0.6958 (t70) REVERT: E 39 ASP cc_start: 0.8067 (t0) cc_final: 0.7698 (m-30) REVERT: E 41 THR cc_start: 0.7057 (p) cc_final: 0.6671 (m) REVERT: E 62 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7343 (mtp85) REVERT: H 20 GLU cc_start: 0.8512 (tt0) cc_final: 0.7712 (pm20) REVERT: H 39 ASP cc_start: 0.8037 (t0) cc_final: 0.7682 (m-30) REVERT: H 41 THR cc_start: 0.7094 (p) cc_final: 0.6715 (m) REVERT: I 20 GLU cc_start: 0.8458 (tt0) cc_final: 0.7661 (pm20) REVERT: I 39 ASP cc_start: 0.8012 (t0) cc_final: 0.7667 (m-30) REVERT: I 41 THR cc_start: 0.7280 (p) cc_final: 0.6867 (m) REVERT: B 12 ILE cc_start: 0.8023 (mt) cc_final: 0.7748 (mp) REVERT: B 65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6840 (t70) REVERT: B 138 SER cc_start: 0.6019 (p) cc_final: 0.5658 (t) REVERT: C 65 ASP cc_start: 0.7272 (m-30) cc_final: 0.6952 (t70) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 0.3207 time to fit residues: 61.0183 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128047 restraints weight = 12587.629| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.11 r_work: 0.3476 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6453 Z= 0.144 Angle : 0.578 6.698 8777 Z= 0.307 Chirality : 0.043 0.154 964 Planarity : 0.004 0.048 1116 Dihedral : 6.999 56.505 905 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 16.43 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.29), residues: 802 helix: 0.54 (0.53), residues: 93 sheet: -0.82 (0.27), residues: 343 loop : -1.09 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.016 0.001 TYR B 13 PHE 0.015 0.001 PHE C 101 TRP 0.010 0.001 TRP C 31 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6438) covalent geometry : angle 0.57458 / 0.31 ( 8747) SS BOND : bond 0.00278 / 0.22 ( 15) SS BOND : angle 1.17953 / 0.70 ( 30) hydrogen bonds : bond 0.03777 / 2.59 ( 250) hydrogen bonds : angle 6.56445 / 4.60 ( 731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7191 (tppt) REVERT: A 96 GLN cc_start: 0.8260 (tt0) cc_final: 0.8037 (tt0) REVERT: A 99 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7798 (tttp) REVERT: E 39 ASP cc_start: 0.7895 (t0) cc_final: 0.7513 (m-30) REVERT: E 41 THR cc_start: 0.6970 (p) cc_final: 0.6618 (m) REVERT: H 39 ASP cc_start: 0.7893 (t0) cc_final: 0.7506 (m-30) REVERT: H 41 THR cc_start: 0.7100 (p) cc_final: 0.6644 (m) REVERT: H 86 GLN cc_start: 0.8608 (tt0) cc_final: 0.8324 (tt0) REVERT: I 39 ASP cc_start: 0.7958 (t0) cc_final: 0.7504 (m-30) REVERT: I 41 THR cc_start: 0.7109 (p) cc_final: 0.6749 (m) REVERT: B 12 ILE cc_start: 0.7963 (mt) cc_final: 0.7716 (mp) REVERT: B 65 ASP cc_start: 0.7291 (m-30) cc_final: 0.6614 (t70) REVERT: B 97 TYR cc_start: 0.8474 (m-80) cc_final: 0.8197 (m-80) REVERT: B 99 LYS cc_start: 0.8264 (ttmt) cc_final: 0.8053 (ttmt) REVERT: B 138 SER cc_start: 0.4590 (p) cc_final: 0.4348 (t) REVERT: C 65 ASP cc_start: 0.7113 (m-30) cc_final: 0.6423 (t70) outliers start: 27 outliers final: 14 residues processed: 170 average time/residue: 0.3447 time to fit residues: 62.8478 Evaluate side-chains 156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 73 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.197145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132318 restraints weight = 18799.737| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.91 r_work: 0.3371 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6453 Z= 0.171 Angle : 0.536 5.547 8777 Z= 0.287 Chirality : 0.043 0.168 964 Planarity : 0.003 0.019 1116 Dihedral : 6.399 56.697 895 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.91 % Allowed : 21.75 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.29), residues: 802 helix: 0.85 (0.53), residues: 93 sheet: -0.64 (0.27), residues: 334 loop : -1.25 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 80 TYR 0.018 0.001 TYR C 13 PHE 0.012 0.001 PHE C 101 TRP 0.014 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 6438) covalent geometry : angle 0.53473 / 0.29 ( 8747) SS BOND : bond 0.00247 / 0.18 ( 15) SS BOND : angle 0.79648 / 0.47 ( 30) hydrogen bonds : bond 0.03131 / 2.18 ( 250) hydrogen bonds : angle 6.07318 / 4.25 ( 731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.6935 (ttmt) cc_final: 0.6713 (mtpt) REVERT: E 39 ASP cc_start: 0.8039 (t0) cc_final: 0.7649 (m-30) REVERT: E 41 THR cc_start: 0.6996 (p) cc_final: 0.6661 (m) REVERT: H 39 ASP cc_start: 0.7980 (t0) cc_final: 0.7565 (m-30) REVERT: H 41 THR cc_start: 0.7105 (p) cc_final: 0.6651 (m) REVERT: I 39 ASP cc_start: 0.8063 (t0) cc_final: 0.7593 (m-30) REVERT: I 41 THR cc_start: 0.7123 (p) cc_final: 0.6755 (m) REVERT: B 12 ILE cc_start: 0.7991 (mt) cc_final: 0.7733 (mp) REVERT: B 34 GLU cc_start: 0.7503 (tt0) cc_final: 0.7246 (tt0) REVERT: B 65 ASP cc_start: 0.7395 (m-30) cc_final: 0.6705 (t70) REVERT: B 97 TYR cc_start: 0.8528 (m-80) cc_final: 0.8311 (m-80) REVERT: B 99 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8127 (ttmt) REVERT: B 138 SER cc_start: 0.4710 (p) cc_final: 0.4495 (t) REVERT: C 65 ASP cc_start: 0.7127 (m-30) cc_final: 0.6572 (t70) REVERT: C 138 SER cc_start: 0.5005 (p) cc_final: 0.4714 (t) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 0.2948 time to fit residues: 51.3799 Evaluate side-chains 153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.196229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130647 restraints weight = 16931.807| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.75 r_work: 0.3390 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6453 Z= 0.208 Angle : 0.557 7.617 8777 Z= 0.295 Chirality : 0.043 0.167 964 Planarity : 0.003 0.024 1116 Dihedral : 6.450 58.802 892 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.54 % Allowed : 22.85 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 802 helix: 1.11 (0.54), residues: 93 sheet: -0.59 (0.27), residues: 331 loop : -1.38 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 62 TYR 0.021 0.002 TYR C 13 PHE 0.012 0.001 PHE C 101 TRP 0.012 0.002 TRP C 31 HIS 0.005 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 6438) covalent geometry : angle 0.55667 / 0.29 ( 8747) SS BOND : bond 0.00164 / 0.12 ( 15) SS BOND : angle 0.51275 / 0.30 ( 30) hydrogen bonds : bond 0.02955 / 2.06 ( 250) hydrogen bonds : angle 5.92682 / 4.16 ( 731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6825 (mmm) cc_final: 0.6018 (tpp) REVERT: A 99 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7549 (tttp) REVERT: A 134 LYS cc_start: 0.6967 (ttmt) cc_final: 0.6696 (mtpt) REVERT: E 39 ASP cc_start: 0.8015 (t0) cc_final: 0.7600 (m-30) REVERT: E 41 THR cc_start: 0.6992 (p) cc_final: 0.6671 (m) REVERT: H 39 ASP cc_start: 0.7915 (t0) cc_final: 0.7489 (m-30) REVERT: H 41 THR cc_start: 0.7061 (p) cc_final: 0.6610 (m) REVERT: I 39 ASP cc_start: 0.7967 (t0) cc_final: 0.7526 (m-30) REVERT: I 41 THR cc_start: 0.7092 (p) cc_final: 0.6746 (m) REVERT: B 12 ILE cc_start: 0.7961 (mt) cc_final: 0.7687 (mp) REVERT: B 65 ASP cc_start: 0.7350 (m-30) cc_final: 0.6659 (t70) REVERT: B 83 MET cc_start: 0.6865 (tpp) cc_final: 0.6571 (mmm) REVERT: C 7 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6937 (tt) REVERT: C 65 ASP cc_start: 0.7232 (m-30) cc_final: 0.6547 (t70) REVERT: C 99 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7901 (ttmt) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 0.3275 time to fit residues: 51.9217 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 59 optimal weight: 0.0000 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.200508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136506 restraints weight = 18851.842| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 4.58 r_work: 0.3412 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6453 Z= 0.113 Angle : 0.502 6.968 8777 Z= 0.267 Chirality : 0.042 0.172 964 Planarity : 0.002 0.023 1116 Dihedral : 5.529 51.587 890 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.91 % Allowed : 23.63 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.29), residues: 802 helix: 1.70 (0.54), residues: 90 sheet: -0.67 (0.27), residues: 340 loop : -1.18 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 80 TYR 0.021 0.001 TYR C 13 PHE 0.011 0.001 PHE C 101 TRP 0.011 0.001 TRP C 31 HIS 0.003 0.001 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6438) covalent geometry : angle 0.50202 / 0.27 ( 8747) SS BOND : bond 0.00167 / 0.13 ( 15) SS BOND : angle 0.47877 / 0.29 ( 30) hydrogen bonds : bond 0.02522 / 1.73 ( 250) hydrogen bonds : angle 5.55756 / 3.91 ( 731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6742 (mmm) cc_final: 0.6021 (tpp) REVERT: A 99 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7642 (tttm) REVERT: E 39 ASP cc_start: 0.8063 (t0) cc_final: 0.7644 (m-30) REVERT: E 41 THR cc_start: 0.6991 (p) cc_final: 0.6702 (m) REVERT: H 39 ASP cc_start: 0.7989 (t0) cc_final: 0.7538 (m-30) REVERT: H 41 THR cc_start: 0.7056 (p) cc_final: 0.6611 (m) REVERT: H 86 GLN cc_start: 0.8621 (tt0) cc_final: 0.8331 (tt0) REVERT: I 9 ILE cc_start: 0.8392 (mt) cc_final: 0.8149 (mt) REVERT: I 39 ASP cc_start: 0.8092 (t0) cc_final: 0.7638 (m-30) REVERT: I 41 THR cc_start: 0.7015 (p) cc_final: 0.6729 (m) REVERT: B 12 ILE cc_start: 0.7957 (mt) cc_final: 0.7682 (mp) REVERT: B 34 GLU cc_start: 0.7481 (tt0) cc_final: 0.7217 (tt0) REVERT: B 65 ASP cc_start: 0.7464 (m-30) cc_final: 0.6810 (t70) REVERT: C 65 ASP cc_start: 0.7178 (m-30) cc_final: 0.6574 (t70) outliers start: 25 outliers final: 14 residues processed: 156 average time/residue: 0.3046 time to fit residues: 51.2426 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 96 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 96 GLN B 100 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.192807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121883 restraints weight = 9687.641| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.83 r_work: 0.3396 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6453 Z= 0.357 Angle : 0.660 8.637 8777 Z= 0.346 Chirality : 0.046 0.159 964 Planarity : 0.004 0.084 1116 Dihedral : 6.084 59.143 889 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.79 % Allowed : 22.69 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.29), residues: 802 helix: 1.38 (0.55), residues: 93 sheet: -0.77 (0.27), residues: 346 loop : -1.42 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 62 TYR 0.026 0.002 TYR C 13 PHE 0.010 0.002 PHE I 55 TRP 0.020 0.003 TRP C 31 HIS 0.007 0.002 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.36 ( 6438) covalent geometry : angle 0.66037 / 0.35 ( 8747) SS BOND : bond 0.00137 / 0.10 ( 15) SS BOND : angle 0.45877 / 0.27 ( 30) hydrogen bonds : bond 0.03133 / 2.19 ( 250) hydrogen bonds : angle 6.05709 / 4.28 ( 731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5188 (mp) REVERT: A 83 MET cc_start: 0.6758 (mmm) cc_final: 0.6313 (tpp) REVERT: A 99 LYS cc_start: 0.8244 (ttmt) cc_final: 0.8008 (ttmt) REVERT: E 39 ASP cc_start: 0.7978 (t0) cc_final: 0.7589 (m-30) REVERT: E 41 THR cc_start: 0.7020 (p) cc_final: 0.6700 (m) REVERT: E 80 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8157 (mmt90) REVERT: H 20 GLU cc_start: 0.8409 (tt0) cc_final: 0.7814 (pm20) REVERT: H 39 ASP cc_start: 0.7898 (t0) cc_final: 0.7486 (m-30) REVERT: H 41 THR cc_start: 0.7103 (p) cc_final: 0.6659 (m) REVERT: I 20 GLU cc_start: 0.8332 (tt0) cc_final: 0.7659 (pm20) REVERT: I 39 ASP cc_start: 0.7940 (t0) cc_final: 0.7557 (m-30) REVERT: I 41 THR cc_start: 0.7074 (p) cc_final: 0.6712 (m) REVERT: I 44 LYS cc_start: 0.8365 (mttt) cc_final: 0.8087 (mtmt) REVERT: B 12 ILE cc_start: 0.7999 (mt) cc_final: 0.7714 (mp) REVERT: B 99 LYS cc_start: 0.8416 (tttp) cc_final: 0.7905 (tttm) REVERT: C 7 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7023 (tt) REVERT: C 99 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7273 (tttp) outliers start: 37 outliers final: 22 residues processed: 151 average time/residue: 0.2989 time to fit residues: 48.9536 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 96 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 33 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 100 ASN C 63 GLN C 100 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.200155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128119 restraints weight = 13595.444| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.33 r_work: 0.3482 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6453 Z= 0.122 Angle : 0.526 6.428 8777 Z= 0.277 Chirality : 0.042 0.168 964 Planarity : 0.003 0.044 1116 Dihedral : 5.434 47.865 889 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.07 % Allowed : 25.51 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.29), residues: 802 helix: 1.93 (0.54), residues: 90 sheet: -0.54 (0.28), residues: 331 loop : -1.35 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.024 0.001 TYR C 13 PHE 0.007 0.001 PHE A 94 TRP 0.017 0.002 TRP C 31 HIS 0.003 0.001 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6438) covalent geometry : angle 0.52644 / 0.28 ( 8747) SS BOND : bond 0.00146 / 0.12 ( 15) SS BOND : angle 0.40568 / 0.25 ( 30) hydrogen bonds : bond 0.02492 / 1.74 ( 250) hydrogen bonds : angle 5.57858 / 3.96 ( 731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6324 (tptt) REVERT: A 83 MET cc_start: 0.6741 (mmm) cc_final: 0.6083 (tpp) REVERT: A 96 GLN cc_start: 0.8233 (tt0) cc_final: 0.7560 (tm-30) REVERT: A 166 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.4559 (pp-130) REVERT: E 39 ASP cc_start: 0.7980 (t0) cc_final: 0.7560 (m-30) REVERT: E 41 THR cc_start: 0.6988 (p) cc_final: 0.6709 (m) REVERT: H 39 ASP cc_start: 0.7911 (t0) cc_final: 0.7463 (m-30) REVERT: H 41 THR cc_start: 0.7047 (p) cc_final: 0.6630 (m) REVERT: H 86 GLN cc_start: 0.8621 (tt0) cc_final: 0.8326 (tt0) REVERT: I 9 ILE cc_start: 0.8379 (mt) cc_final: 0.8131 (mt) REVERT: I 39 ASP cc_start: 0.8006 (t0) cc_final: 0.7555 (m-30) REVERT: I 41 THR cc_start: 0.7029 (p) cc_final: 0.6706 (m) REVERT: B 12 ILE cc_start: 0.7914 (mt) cc_final: 0.7557 (mp) REVERT: B 96 GLN cc_start: 0.8289 (tt0) cc_final: 0.7994 (tm-30) REVERT: B 99 LYS cc_start: 0.8178 (tttp) cc_final: 0.7551 (tttp) REVERT: C 99 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7178 (tttp) outliers start: 26 outliers final: 15 residues processed: 151 average time/residue: 0.2897 time to fit residues: 47.5800 Evaluate side-chains 150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN I 124 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.198760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126583 restraints weight = 13424.346| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.25 r_work: 0.3462 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6453 Z= 0.159 Angle : 0.547 7.203 8777 Z= 0.285 Chirality : 0.043 0.162 964 Planarity : 0.003 0.041 1116 Dihedral : 5.587 48.433 887 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.54 % Allowed : 25.98 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.29), residues: 802 helix: 2.01 (0.54), residues: 90 sheet: -0.68 (0.27), residues: 346 loop : -1.28 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 62 TYR 0.024 0.002 TYR C 13 PHE 0.012 0.001 PHE B 140 TRP 0.023 0.002 TRP A 31 HIS 0.004 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 6438) covalent geometry : angle 0.54727 / 0.29 ( 8747) SS BOND : bond 0.00146 / 0.11 ( 15) SS BOND : angle 0.38264 / 0.23 ( 30) hydrogen bonds : bond 0.02535 / 1.78 ( 250) hydrogen bonds : angle 5.53188 / 3.92 ( 731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7307 (ttpt) cc_final: 0.6323 (tptt) REVERT: A 83 MET cc_start: 0.6668 (mmm) cc_final: 0.6014 (tpp) REVERT: A 96 GLN cc_start: 0.8274 (tt0) cc_final: 0.7508 (tm-30) REVERT: A 166 MET cc_start: 0.5413 (ppp) cc_final: 0.4494 (pp-130) REVERT: E 39 ASP cc_start: 0.7979 (t0) cc_final: 0.7585 (m-30) REVERT: E 41 THR cc_start: 0.6996 (p) cc_final: 0.6702 (m) REVERT: H 39 ASP cc_start: 0.7918 (t0) cc_final: 0.7468 (m-30) REVERT: H 41 THR cc_start: 0.7086 (p) cc_final: 0.6646 (m) REVERT: I 39 ASP cc_start: 0.7955 (t0) cc_final: 0.7520 (m-30) REVERT: I 41 THR cc_start: 0.7027 (p) cc_final: 0.6684 (m) REVERT: B 12 ILE cc_start: 0.7872 (mt) cc_final: 0.7532 (mp) outliers start: 29 outliers final: 18 residues processed: 153 average time/residue: 0.3221 time to fit residues: 53.2828 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 90 GLN I 122 ASN I 124 ASN B 100 ASN C 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.200803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128041 restraints weight = 14480.854| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.40 r_work: 0.3477 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6453 Z= 0.126 Angle : 0.543 8.700 8777 Z= 0.280 Chirality : 0.043 0.164 964 Planarity : 0.003 0.034 1116 Dihedral : 5.426 44.258 887 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.13 % Allowed : 27.23 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.29), residues: 802 helix: 2.15 (0.54), residues: 90 sheet: -0.54 (0.27), residues: 337 loop : -1.25 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 62 TYR 0.025 0.002 TYR C 13 PHE 0.011 0.001 PHE B 140 TRP 0.030 0.002 TRP A 31 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6438) covalent geometry : angle 0.54323 / 0.28 ( 8747) SS BOND : bond 0.00159 / 0.12 ( 15) SS BOND : angle 0.50704 / 0.31 ( 30) hydrogen bonds : bond 0.02468 / 1.72 ( 250) hydrogen bonds : angle 5.43307 / 3.85 ( 731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6323 (tptt) REVERT: A 83 MET cc_start: 0.6701 (mmm) cc_final: 0.6025 (tpp) REVERT: A 96 GLN cc_start: 0.8235 (tt0) cc_final: 0.7465 (tm-30) REVERT: A 99 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7502 (tttm) REVERT: A 166 MET cc_start: 0.5229 (ppp) cc_final: 0.4325 (pp-130) REVERT: E 39 ASP cc_start: 0.7981 (t0) cc_final: 0.7558 (m-30) REVERT: E 41 THR cc_start: 0.6969 (p) cc_final: 0.6689 (m) REVERT: H 39 ASP cc_start: 0.7936 (t0) cc_final: 0.7485 (m-30) REVERT: H 41 THR cc_start: 0.7057 (p) cc_final: 0.6646 (m) REVERT: I 39 ASP cc_start: 0.7993 (t0) cc_final: 0.7521 (m-30) REVERT: I 41 THR cc_start: 0.7023 (p) cc_final: 0.6707 (m) REVERT: B 12 ILE cc_start: 0.7822 (mt) cc_final: 0.7566 (mp) REVERT: B 34 GLU cc_start: 0.7395 (tt0) cc_final: 0.7153 (tt0) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.3262 time to fit residues: 51.9739 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 122 ASN I 124 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.203216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134908 restraints weight = 15894.701| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.64 r_work: 0.3499 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6453 Z= 0.105 Angle : 0.529 11.001 8777 Z= 0.273 Chirality : 0.043 0.160 964 Planarity : 0.002 0.027 1116 Dihedral : 4.866 37.559 885 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.35 % Allowed : 27.39 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.29), residues: 802 helix: 2.24 (0.54), residues: 90 sheet: -0.51 (0.27), residues: 346 loop : -1.16 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 62 TYR 0.023 0.001 TYR C 13 PHE 0.010 0.001 PHE B 140 TRP 0.030 0.002 TRP A 31 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6438) covalent geometry : angle 0.52923 / 0.27 ( 8747) SS BOND : bond 0.00205 / 0.17 ( 15) SS BOND : angle 0.43798 / 0.27 ( 30) hydrogen bonds : bond 0.02390 / 1.65 ( 250) hydrogen bonds : angle 5.31396 / 3.76 ( 731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6172 (tptt) REVERT: A 83 MET cc_start: 0.6729 (mmm) cc_final: 0.5900 (tpp) REVERT: A 96 GLN cc_start: 0.8201 (tt0) cc_final: 0.7406 (tm-30) REVERT: A 99 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7474 (tttm) REVERT: A 166 MET cc_start: 0.5080 (ppp) cc_final: 0.4020 (pp-130) REVERT: E 39 ASP cc_start: 0.8003 (t0) cc_final: 0.7652 (m-30) REVERT: E 41 THR cc_start: 0.6962 (p) cc_final: 0.6710 (m) REVERT: H 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7510 (m-30) REVERT: H 41 THR cc_start: 0.7014 (p) cc_final: 0.6589 (m) REVERT: I 39 ASP cc_start: 0.8023 (t0) cc_final: 0.7544 (m-30) REVERT: I 41 THR cc_start: 0.6938 (p) cc_final: 0.6643 (m) REVERT: B 12 ILE cc_start: 0.7764 (mt) cc_final: 0.7509 (mp) REVERT: B 34 GLU cc_start: 0.7336 (tt0) cc_final: 0.7100 (tt0) REVERT: C 34 GLU cc_start: 0.7517 (tt0) cc_final: 0.7202 (tt0) REVERT: C 99 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7493 (tttp) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.3342 time to fit residues: 52.3792 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN H 122 ASN I 122 ASN B 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.202393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136213 restraints weight = 16724.959| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.85 r_work: 0.3464 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6453 Z= 0.124 Angle : 0.547 11.213 8777 Z= 0.281 Chirality : 0.043 0.158 964 Planarity : 0.003 0.028 1116 Dihedral : 4.893 37.824 885 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.66 % Allowed : 27.23 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.29), residues: 802 helix: 2.27 (0.54), residues: 90 sheet: -0.45 (0.27), residues: 346 loop : -1.18 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 17 TYR 0.021 0.001 TYR B 13 PHE 0.012 0.001 PHE C 140 TRP 0.042 0.003 TRP C 31 HIS 0.003 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6438) covalent geometry : angle 0.54784 / 0.28 ( 8747) SS BOND : bond 0.00183 / 0.15 ( 15) SS BOND : angle 0.35693 / 0.22 ( 30) hydrogen bonds : bond 0.02430 / 1.69 ( 250) hydrogen bonds : angle 5.36895 / 3.78 ( 731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.33 seconds wall clock time: 45 minutes 5.01 seconds (2705.01 seconds total)